web 2.0 e ricerca scientifica - web 2.0 and scientific research
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Web 20 e ricerca
(Giovanni M DallOlio ndash raduno molecularlab 2008)
Cosa eacute Web 20
bull Blogs
bull Rss Feedsbull Wikis (wikipedia)
bull Social Bookmarking (delicious)bullMultimediashysharing systems (Youtube shygt videos
Flickr shygt photos lastfm shygt music )
These and others are called Web 20 Technologies[1]
The common point in all web 20 technologies is that they help people in sharing informations and opinions
Scientists also need to share and exchange their informations and opinions[2]
Lets see a few examples of some of the Web 20 applications actually used in the scientific community
What is Web 20
I - Blogs
I blog sono lequivalente di un diario personale reso pubblico su Internet
Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]
Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali
I - Blogs
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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Cosa eacute Web 20
bull Blogs
bull Rss Feedsbull Wikis (wikipedia)
bull Social Bookmarking (delicious)bullMultimediashysharing systems (Youtube shygt videos
Flickr shygt photos lastfm shygt music )
These and others are called Web 20 Technologies[1]
The common point in all web 20 technologies is that they help people in sharing informations and opinions
Scientists also need to share and exchange their informations and opinions[2]
Lets see a few examples of some of the Web 20 applications actually used in the scientific community
What is Web 20
I - Blogs
I blog sono lequivalente di un diario personale reso pubblico su Internet
Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]
Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali
I - Blogs
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
The common point in all web 20 technologies is that they help people in sharing informations and opinions
Scientists also need to share and exchange their informations and opinions[2]
Lets see a few examples of some of the Web 20 applications actually used in the scientific community
What is Web 20
I - Blogs
I blog sono lequivalente di un diario personale reso pubblico su Internet
Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]
Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali
I - Blogs
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
I - Blogs
I blog sono lequivalente di un diario personale reso pubblico su Internet
Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]
Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali
I - Blogs
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 46
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- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
I blog sono lequivalente di un diario personale reso pubblico su Internet
Ognuno eacute libero di scrivere quello che vuole nel proprio blog storie personali opinioni etc [3]
Recentemente si sono diffusi i blog a contenuti tecnico in cui vengono trattati argomenti tecnici anzicheacute personali
I - Blogs
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
The fungalgenomeorg Blog fungalgenomeorg eacute un blog sui funghi e sulla
genetica dei microrganismi unicellulari[5]
Ogni settimana gli autori postano qualche notizia su questo campo commentano un articolo pubblicato o una scoperta recente etc[6]
Puograve essere piugrave semplice tenersi aggiornarti sulla genetica de funghi in questo modo piuttosto che seguire le riviste specializzate
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 54
- Pagina 55
-
the fungalgenomeorg Blog
(httpwwwfungalgenomeorgblog)
programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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programming4scientistscom
Blog di bioinformatica programmazione per scienziati
Lautore fornisce consigli e tutorial su come programmare per scienziati
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Nature Blogs
Nature ha messo su una rete di blogs dedicati a neuroscienze tecnologia virologia genetica etc
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Nascent
Blog sulla tecnologia web appartenente al circuito di Nature
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
II - Wikis
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
- Pagina 11
- Pagina 12
- Pagina 13
- Pagina 14
- Pagina 15
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- Pagina 41
- Pagina 42
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- Pagina 44
- Pagina 45
- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
A wiki is a website that allows visitors to add remove and otherwise edit and change content
Like Wikipedia (httpenwikipediaorg)[7]
II - Wikis
Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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Wikipedia
(httpenwikipediaorg)
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Build your Labs Wiki
The software that run wikipedia is called MediaWiki and is released under a free license [8]
This means you can download it (the templates of the wiki without its contents) to use it for your own purposes
So you can create a website with the same functionalities and interface of wikipedia but with your own content
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Build your own wiki - examples(Alternative Splicing Wiki[9])
(This is a wiki I use on my laptop to organize my work about alternative splicing)
Alternative splicing analysis tools
Alternative splicing analysis tools
DatabasesArticles
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Build your own wiki - examples(appunti di bioinformatica libera[10])
(httpbioinformaticiorgappunti - a wiki by some Italian students of bioinformatics)
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Wiki Technology in Bioinformatics Examples (I)
openwetware (httpopenwetwareorg) is a huge wiki created in 2005 in the MIT institute which collects protocols resources courses discussions about wet biology and bioinformatics research
the annotation of 12 drosophila spp genomes has been done by wiki (httpranalblgovdrosophilawiki)
There have been some discussions about the use of wikis to improve genome annotation (2 articles on Nature and on nodalpoint [11])
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
OpenWetWare
(httpopenwetwareorg)
Protocols (How to make a PCR how to design primers etc)
Labs home pages
Resources (tutorials etc)
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
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- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
AAAWiki (Annotation of 12 Drosophila spp genomes)
(httpranalblgovdrosophilawiki)
Announcements
DataPapers
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
- Pagina 11
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- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Wiki Technology in Bioinformatics Examples (II)
WikiOmics (httpwikiomicsorg) is a wiki for the bioinformatics community providing tutorials and reviews
Manatee (httpmanateesfnet) is a genome evaluationannotation tool which allows scientists to make functional assignments on genes and sequences
GenBank (httpwwwncbinlmnihgovGenbankTPAshyInf) offers a system to submit thirdshyparty annotation to sequences)
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
WikiOmics(wikipedia for bioinformaticists)
(httpwikiomicsorg)
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
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- Pagina 54
- Pagina 55
-
Wiki Technology in Bioinformatics Examples (III)
GONUTS (httpgowikitamueduGOwiki) is a wiki to provide third party annotation and documentation to the GeneOntology (GO) terms
EcoliWiki (httpecoliwikinetcolipedia) is a prototype of a wiki to annotate Ecoli genome and metabolic network
The Fungalgenome website (httpfungalgenomeorgwiki ) also has a wiki to organize fungal genomes annotation
The SynapticLeap (httpthesynapticleaporg) hosts some research communities
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
- Pagina 11
- Pagina 12
- Pagina 13
- Pagina 14
- Pagina 15
- Pagina 16
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- Pagina 39
- Pagina 40
- Pagina 41
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- Pagina 44
- Pagina 45
- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Wiki Technology in Bioinformatics Examples (IV)
WikiReviews (httptinyurlcom26c6m8) at OpenWetWare is to provide comments on reviews
The Saccharomyces Genome Database (httpyeastgenomeorg) has just started a wiki for the community working on yeast (httpwikiyeastgenomeorg) [12]
BioWiki (httpbiowikiorg) hosts other bioinformatics projects
WikiSurgery (httpwwwwikisurgerycom) is a free surgical encyclopedia for surgeons and patients
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
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-
FungalGenome Wiki
(httpfungalgenomeorgwiki)
Projects - descriptions
Protocols
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
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- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
III - Social-Bookmarking
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
- Pagina 11
- Pagina 12
- Pagina 13
- Pagina 14
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- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
III - Social-Bookmarking
Social Bookmarking meansndash When I find an interesting websitearticledocument I
share its address with other people ndash or with the other members of the lab(s)[13]
ndash Other people can add their comments and tags to it
ndash Eventually a third person can be in charge of organize and curate those collections of bookmarks
Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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Social Bookmarking in Science
The most used services arendash deliciousndash Connoteandash CiteULikendash Hubmed (Tags system)[14]
delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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delicious
It is the most known Social Bookmarking Service
It is not designed to manage publications only bookmarks
Easy to configure and use (firefoxepiphany extension)
Some scientists use it to bookmark RSS feeds from connotea or pubmedhubmed searches or from other scientific websites[15]
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Social Bookmarking ndash how does it work
You have to register to the website which offers the social bookmarking service (eg delicious connotea etc)
you need to configure your webshybrowser by adding a special button to it (some firefox extensions facilitate this)
When you find an interesting article you click on that button and follow the instructions
Bookmarks are saved in a webserver (a publicly accessible computer) where they are accessible to everyone you allow
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
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- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Social Bookmarking in ScienceConnotea
Connotea is an online social bookmarking service for scientists created by Nature Publishing Group
It allows to post articles as well as web documents
It automatically recognizes metadata like title author abstract when posting an article
Slightly more difficult to configure and use (no firefox extension)[16]
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Connotea Screenshots (I)(main page)
(httpwwwconnoteaorg)
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Connotea Screenshots (II)(searching for tags)
(httpwwwconnoteaorgsearchq=22alternative+splicing22)
Search Interface
Search Results
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Connotea Screenshots (III)(posting an article)
(httpwwwconnoteaorg - note the automatic recognition of title and authors)
Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
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Social Bookmarking in ScienceCiteULike
CiteULike is another social referencingbookmarking tool for scientists
Its not opensource but its not related to any publishing group (eg Nature)
Like Connotea it allows to navigate into tags and people to importexport references in BibTeX etc
CiteULike and Connotea have different databases and users[17]
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
CiteULike Screenshots (I)(searching between tags)
(httpwwwciteulikeorg)
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 53
- Pagina 54
- Pagina 55
-
Connotea Screenshots (II)(posting an article)
(httpwwwciteulikeorg - note the automatic recognition of title and authors)
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
- Pagina 9
- Pagina 10
- Pagina 11
- Pagina 12
- Pagina 13
- Pagina 14
- Pagina 15
- Pagina 16
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
IV Scientific Communities
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
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- Pagina 46
- Pagina 47
- Pagina 48
- Pagina 49
- Pagina 50
- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Comunitagrave scientifiche
Una comunitagrave online eacute un luogo in cui ogni utente eacute distinto da un proprio profilo personale
Esistono anche esperimenti di comunitagrave scientifiche che si rifanno a facebookmyspaceetc
myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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myExperiment
Su myExperiment I ricercatori possono mettere in condivisione i loro protocolli bioinformatici
Scarica la sequenza da ncbi shygt lancia blast shygt prendi i 10 migliori risultati shygt etc
Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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Esempi di workflow da myExperiment
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 4
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- Pagina 51
- Pagina 52
- Pagina 53
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- Pagina 55
-
Second Life
Second Nature eacute una comunitagrave scientifica basata su Second Life un gioco multiplayer online
Si organizzano conferenze ed esposizioni virtuali e si puograve discutere con altri esperti
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Molecularlab )
Non esistono molte comunitagraveforum scientifici attivi
Molti sono semishyabbandonati o con poca frequenza
A volte si preferiscono le mailing list
Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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Scivee
V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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V - RSS Feed
V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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V - RSS Feed
RSS Feeds are an instrument used by webmasters to notify users about changes into their website[18]
Imagine an online newspaper site users can use rss feeds to be notified when a new article appears
Rss Feeds can be also used to track new articles new results from a pubmedhubmed search new blog posts and so on
how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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how do I use Rss Feeds III
When you see this symbol
on a website it means it offers rss feeds You can click on it and follow the instructions to
subscribe to the sites rss feeed
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 2
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-
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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how do I use Rss Feeds - examples
Rss Feeds Button(click on it to subscribe)
how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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how do I use Rss Feeds IIII
Do I need to install any programndash Upshytoshydate browsers (Firefox Opera etc) have
builtshyin capabilities to read rss feedsndash Otherwise you can use a Rss Reader applicationndash Rss Readers Applications are more comfortable ndash
they have a better interface they can show notifications on your desktop etc
ndash Examples Liferea Blam Mugshot (see httpenwikipediaorgwikiRss_reader)
How to use RSS Feeds[19] httpwwwanswerscomhow20to20use20rss20feeds20tutorialff=1
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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-
Rss Feeds instant notificationsof new articles on your desktop (I)
(liferea a rss reader)
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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- Pagina 2
- Pagina 3
- Pagina 4
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-
Liferea an RSS Reader
(This is liferea on my computer)
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
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- Pagina 51
- Pagina 52
- Pagina 53
- Pagina 54
- Pagina 55
-
Rss Feeds instant notificationsof new articles on your desktop (II)
(mugshot another rss reader)
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
- Pagina 1
- Pagina 2
- Pagina 3
- Pagina 4
- Pagina 5
- Pagina 6
- Pagina 7
- Pagina 8
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-
References [1] Def Web 20 httpenwikipediaorgwikiWeb_20
httpwwwgoogleitsearchq=define3A22web202022amp httpwwwanswerscomweb2020
[2] Web 20 and Science discussions httpwwwnodalpointorgnode1749 (Nature The impact of Web 20 on Science and publishing) httpwwwnodalpointorg20061129web_2_0_and_science_video_presentations_from_embl httpopenwetwareorgwikiScience_20 (Openwetware) httpopenwetwareorgwikiScience_20Brainstorming (Openwetware)httpwwwbmjcomcgicontentextract33375821283 (how Web 20 is changing medicine)httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x (The emerging Web 20 social software )
[3] Def Weblog httpenwikipediaorgwikiWeblog httpanswerscomweblog httpgooglecomsearchq=defineweblog
[4] Bioinformatics Blogs List httpwikinodalpointorgblogs I recommend BioBlogs (httpbioblogswordpresscom) and nodalpoint (httpnodalpointorg)
[6] A few discussions about the topic blog and science
ndash Blogs and Wikis Are Valuable Software Tools for Communication Within Research Groups Sauer et al 2005 (httpwwwblackwell-synergycomdoifull101111j1525-1594200429005xcookieSet=1)
ndash httpwwwnodalpointorgnode1623 and others on nodalpoint
[7] Just in case httpenwikipediaorgwikiWikipedia
[8] Mediawiki is the software ran by Wikipedia There are other softwares avaible for wiki I suggest to read this article httpenwikipediaorgwikiComparison_of_wiki_software However almost all of the scientific wikis I know use Mediawiki with the advantage of having some additional plugins like Biblio (httpgenomeimimeswikiskinsmonobookexternalpng) to handle BibTeX referencesSee also httpwikiomicsorgwikiIdeas
References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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References (continued) [9] Alternative Splicing Wiki Currently accessible only from my laptop please ask me if interested
[10] Appunti di bioinformatica libera means Notes of free Bioinformatics Its a project to collect tutorials and resources about what its possibile to do in bioinformatics using only free accessible resources )
[11] Discussions and articles about using Wikis to improve genome annotation
ndash httpnodalpointorg20070212genome_wiki
ndash httpfungalgenomesorgblog200702wikis-for-genome-reannotation
ndash httpgenomebiologycom200781102
[12] Yeast Genome Wiki this has appeared on 12th of March when I was still writing this presentation ) httpfungalgenomesorgblog200703sgd-community-annotation
[13] Discussions about using Social Bookmarking in Science
ndash httpwwwblackwell-synergycomdoiabs101111j1471-1842200700701x many on nodalpoint
[14] delicious connotea citeulike hubmed(tags) The hubmed tags system is actually a little experimental
[15] Scientists use delicious to bookmark rss feeds ehi why dont you look at this discussion httpnodalpointorg20070307what_about_using_mugshot_in_bioinformatics
[16] Configure connotea tutorial httpwwwconnoteaorggetting_started_other httpwwwconnoteaorgguide
[17] Connotea and CiteULike have different users
[18] Rss Feeds httpenwikipediaorgwikiRss_Feed
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