modern tools & rationales for 21st century research
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Modern Tools & Rationales for 21st Century Research
Ross Mounce (@RMounce)Natural History Museum, London
European Phycological Congress, Student Symposium 2015-08-27
XKCD 1179 on ISO 8601
Slides available online: slideshare.net/rossmounce
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Sharing is caring
If you wish, please do share, tweet, discuss, re-use this talk
I'm a firm believer that research should be open by default,
specifically including conference talks & posters!!!
Previous meetings to have got this wrong include: SVP '14 and ESA '15, as documented in Nature News recently… http://www.nature.com/news/conference-tweeting-rule-frustrates-ecologists-1.18207
#EPC6
Twitter & other social media are legitimate tools of great utility in academia. Tweet your talk slides & you'll get a much wider audience for your talk!
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Open, online benefits you
I bet more people have read Seth's poster than any other poster here that hasn't been tweeted
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Open, online benefits you
Nature Communications Open (blue) vs Paywalled (orange),
article views per day
Mean: Open
Mean: Paywalled
DOI: 10.1007/s11192-015-1547-0
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Open, online benefits you
Piwowar HA, Vision TJ. (2013) Data reuse and the open data citation advantage. PeerJ 1:e175
“...open data citation benefit for this sample to be 9%”
relative to papers providing no public data, for gene expression microarray data
10.7717/peerj.175/fig-2See also previous work by Piwowar:10.1371/journal.pone.0000308
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Open, online benefits you
Because the software is open source, online I could look at it and contribute suggested improvements
Users can easily report issues / bugs & feature requests
Demonstrate that people are interested in your software
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Research tools are rapidly improving
Image credit:https://innoscholcomm.silk.co/
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Analysis tools and their communities
These are my favourites, in no particular order.They are tools AND friendly communities. Important.
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Supp. Data Needs to DieFrom the 1990s to 2010s, online supplementary data was used as a way of dumping data online in an ad hoc manner... It was available *shrugs*
Traditional, journal-hosted supplementary files bury data. Additional files are bunged online with little or no additional metadata describing them.
Thus typically, SI isn't searchable. That's a huge problem
Data should be FAIR:
Findable, Accessible, Interoperable, Re-usable
It should be findable independent of the research article
https://www.force11.org/group/fairgroup
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Data sharing platforms
https://zenodo.org/http://figshare.com/http://datadryad.org/
Free-to-use but commercialFree-to-use, CERN backedNot-for-profit
Not-for-profit,Better curated
Charges to keep sustainable
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Data Standards & Data File Formats
Adhere to existing standards! e.g. 2015-08-27 for dates
xkcd 927 on standards
ISO 8601
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Intelligent data papers allow databases to automatically pull-in your data
Many publishers (e.g. Pensoft) intelligently markup data papers so that the data can be automatically ingested into appropriate db's on the day of publication!
Data
data
BiodiversityData Journal
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Those who share data, do better science
Wicherts, J. M., Bakker, M. & Molenaar, D. (2011) Willingness to share research data is related to the strength of the evidence and the quality of reporting of statistical results. PLoS ONE 6, e26828+ URL http://dx.doi.org/10.1371/journal.pone.0026828
The authors examined psychological papers for the quality of statistical reporting & asked the authors of those papers for the full data underlying the reported results. Generally, those who shared, had more statistically robust, reproducible results.
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“Email the author for data” - doesnt work
Wicherts JM, Borsboom D, Kats J, Molenaar D (2006) The poor availability of psychological research data for reanalysis. American Psychologist 61: 726–728 link
A well-known problem, which I myself have also faced many times!!!
Many legacy journals unfortunately still pretend that “email the author” is still acceptable.
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Authoring Tools
Microsoft Word is crap.
Publishers have to spend significant time & effort (= $$$) converting MS Word documents into scholarly publications. Citation styling is stupid too.
Many problems could easily be avoided through use of better authoring tools:
http://biodiversitydatajournal.com/
https://paperpile.com/
+ ShareLatex, BlueLatex, FidusWriter, RVRite...
https://www.authorea.com/ https://www.overleaf.com/
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Discovery Tools
Finding & obtaining access to research isn't easy. These tools can help
https://openaccessbutton.org/
Browser-plugin to help find you free access versions of paywalled research articles
http://www.sparrho.com/
https://www.pubchase.com/
Sparrho & PubChase provide personalised literature recommonedations, like Google Scholar but with more flexibility
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Preprint platforms
A brilliant way of getting your article out there early & in a non-paywalled way
https://peerj.com/preprints/http://biorxiv.org/
http://arxiv.org/
Background reading: The Case for Open Preprints in Biology (2013) PLOS Biology
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Open Access Journals
http://biodiversitydatajournal.com/https://peerj.com/
There are thousands out there. But these are my picks:
$99 per author, lifetime publishing
High-tech, integrated publishing from Pensoft
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PeerJ is the epitome of modern, efficient publishing
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A quick reminder of the cost of paywalls(per year, for 2014)
Institute Total Subscriptions (£)1: University of Manchester 3,205,7022: UCL 3,052,1703: University of Cambridge 2,963,8214: University of Nottingham 2,578,7165: Imperial College London 2,472,5306: University of Bristol 2,395,6547: University of Birmingham 2,178,5588: University of Oxford 2,153,8409: University of Glasgow 2,062,35310: Cardiff University 2,007,977
Source FOI requests, peer-reviewed here: http://f1000research.com/articles/3-274/v3
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In Summary
There are a wealth of new, better tools out there. Use them!
Share: Data, Code, Presentations, Posters, Grant Proposals, Preprints, and Papers
Opening-up your work has benefits to you.
Thank you for your time!