clotho for users
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Welcome to ClothoGuide for users
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Starting Up
When you start up Clotho, youllsee some windows. In the trialversion of Clotho, you should beseeing
The Dashboard
Error Reporter
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Starting Up The Error Reporter justprovides the messagestream from the software.
You can ignore it (justminimize it and pretend its
not there). Once you getcomfortable with Clotho,
youll find its useful forknowing whats going on
behind the scenes.
You can also use it to senderror messages to theClotho development team.
Error Reporter
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Starting Up
The Dashboard allows you to doseveral things:
Connect to the database Launch Tools Manage plugins Change the current user
The Dashboard
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Connecting to the Database
Alright, lets try connecting to
the database. Click the Clothologo to connect:
The Dashboard
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Connecting to the Database
Alright, lets try connecting to
the database. Click the Clothologo to connect:
The Dashboard
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Launching Tools
The Dashboard
Youll notice that this little circle
turns green once youre
connected
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Launching Tools
The Dashboard
Many Clotho tools wont launch
until youre connected.
Now that were connected, letstry launching a tool.
These icons are your tools.
Double click one to launch it.
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Launching Tools
The Dashboard
Tools are Apps, andanyone can write them.Each one behaves
differently, so we wont gofurther with Collection Viewfor now.
This one prompts you to
pick a Collection to view.
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Starting Up
Actually, the Dashboard and theError Reporter are also Apps.
They are Widgets
The Dashboard
Error Reporter
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Starting Up
Like Tools Widgets can bewritten by anyone and added andremoved from your installation ofClotho
The Dashboard
Error Reporter
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Starting Up
The special property of a Widgetis that they get loaded at startup.However, you can disable themfrom the Plugin Manager
The Dashboard
Error Reporter
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Plugin Manager
The Dashboard
To add an App, just dragand drop the file for theApp onto the Dashboard.
To manage your Apps,youll use the pluginmanager.
Plugin Manager is itself aTool App that can bechanged.
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Plugin Manager
The Dashboard
To launch the pluginmanager, click manage
plugins
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Plugin Manager
The DashboardThat pops up the pluginmanager
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Plugin ManagerPlugin manager allows you to:
Remove Apps Set which Widgets launch on startup Register Viewers on different object types
Set the default database connection
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Plugin Manager
For further information on how to do thesethings, click the help icon.
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The Right Click Popup
The last major Core-encoded visiblecomponent is the right-click popup menu
Many Apps will enable you to right click onsomething to popup up this menu.
Lets take a look at what happens when we
right click on a line of a Collection Viewwindow
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The Right Click Popup
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The Right Click Popup
The right click popup allows you to:
Save, update, or revert the object you clicked on Undo / Redo recent changes to the object
Copy the object to the clipboard Paste whatevers on the clipboard into the object View, add, or remove search tags associated with the
object
Launch a viewer on the object Jump to other objects linked by this object
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Clotho Plugins
Speaking of Viewers, these are another type of App.
Many Tools are also Viewers. Their essential property isthat they launch on one object. In total, there are 7distinct types of Clotho plugins:
Widgets Tools Viewers
Connections Formats Grammars Algorithms
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Clotho Objects
So, weve covered plugins. The other major ingredientin Clotho are its objects. The objects are your data.Things like Biobrick parts and vectors, plasmids,samples, strains, and experimental data are all
encapsulated by these objects.
Beyond just existing in Clotho, these objects link to oneanother. Lets go through each one currently supported
and see what its linked to.
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Parts
Parts are like BioBricks.
They have a sequence and aformat. The format is thestandard like RFC 10. The
sequence must obey theformat or Clotho will reject thedata.
Parts also have an author. FORMAT
PERSON NUCSEQ
PART
GRAMMAR
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Parts
Parts can be basic orcomposite just like youdexpect with BioBricks.
Grammar isnt implemented
yet, but it deals with the part ofspeech of the Part.
FORMAT
PERSON NUCSEQ
PART
GRAMMAR
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Features
Features are like Parts. Thedistinction can be confusing,but I think once you startthinking this way youll realize
you were already thinking this
way.
Features represent biologicalprimitives while Parts
represent compositionprimitives.
FORMAT
PERSON NUCSEQ
FEATURE
FAMILY
NOTE
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Features
To understand it, lets think about Registry partBBa_I0500 Inducible pBad/araC promoter
I0500 would be a Part as its a useful unit for compositionwith a precise sequence and there are rules about howto combine it with other Parts. Moreover, its a Basic Part
since it cant be reduced to shorter RFC10 Parts.
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Features
The AraC coding sequenceoriented on the reverse strand isa Feature that is mapped ontothis Part.
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Features
What Features are present in aPart can be subjective. Also, theycan be overlapping
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Vectors
Vectors are a lot like parts.They are the backboneportion of your plasmids.
They are also used to
describe sites in a genome(yeah, kindov weird, I know,but it does in the end makesense).
All vectors are basic.FORMAT
PERSON NUCSEQ
VECTOR
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Oligos
Oligos are lightweightsequence-linked objects fordescribing the sequence,name, and description of anoligonucleotide.
Like Part, Vector, Feature,and Plasmid, Oligos refer totheoretical objects, not your
physical samples of oligoDNA. Those are somethingelse.
PERSON NUCSEQ
OLIGO
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Plasmids
Plasmids are compositionsof one Part and one Vector.
Since a Vector can refer toan episomal DNA or a site in
the genome, the plasmidarchitecture can describeboth the DNAs floatingaround as well as a genome
modification. FORMAT
PERSON NUCSEQ
PLASMID
PART
VECTOR
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Strains
Strains refer to compositionsof cells. Like Parts, they canbe Basic or Composite.
Composite Strains are
described as a Basic Strainplus a list of Plasmids(episomal or genomic).
You describe mutations inthe genome orknockouts/knockins usingthe same Plasmidframework.
PERSON PLASMID
STRAIN
STRAIN
NOTE
ATTACHMENT
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Sample
Samples are aliquots ofliquid. Samples are alwaysin a Container.
Experimental data can map
onto samples.
Samples can keep track oftheir parent samples.
PERSON CONTAINER
SAMPLE
SAMPLE_DATA
SAMPLE
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Plasmid Samples
Samples of Plasmids likeminipreps are morespecifically PlasmidSamples.
They then also point to aPlasmid composition and asource Strain.
PERSON CONTAINER
SAMPLE
SAMPLE_DATA
SAMPLE
PLASMID
STRAIN
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Strain Samples
Samples of Cells like -80stocks are more specificallyStrainSamples.
They then also point to aStrain composition.
PERSON CONTAINER
SAMPLE
SAMPLE_DATA
SAMPLESTRAIN
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Oligo Samples
Samples of Oligos like thestuff in the tube you got fromIDT are OligoSamples.
They then also point to anOligo.
PERSON CONTAINER
SAMPLE
SAMPLE_DATA
SAMPLEOLIGO
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Containers
Containers can be empty,but at most have oneSample in them.Containers mean both the
wells of a 96-well plateand free tubes likeEppendorf tubes or 2Dbarcode tubes.
Containers can be inplates but dont have to.
CONTAINER
SAMPLE
PLATE
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Plates
Plates contain an array ofcontainers that may ormay not be populated withcontainers.
Plates all have aPlateType which describesits configuration.
CONTAINER
PLATE_TYPE
PLATE
PERSON
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Persons
Many objects have anauthor held as a Personobject.
Persons belong to labswhich belong toinstitutions. Labs alsohave a Person as their PI.
Each Person has apersonal Collection and aBiography in the form of aWikiText
LAB
PERSON
INSTITUTION
WIKITEXT
COLLECTION
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Collections
Collections are bundles of otherClotho objects. So, anything,even another Collection, can beput into a Collection.
Collections will often be returnedas the container of a list of objectsby operations such as searches.
You can also use them toorganize your information intorelated groups of things.
COLLECTION
(All types)
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Notes
Notes are for containinginformation aboutbiological things.
Strains, Features, andFamilies all hold links toNotes.
They have a list of
Factoids and a WikiTextfor putting a description ofits contents.
NOTE
FACTOIDWIKITEXT
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Factoids
Factoids are a nugget ofinformation related to aDOI reference such as awebsite, a pubmed-loggedpaper, patents, or a realDOI.
The reference object isretrieved from the web, so
it seems like Clotho keepstrack of it (even though itdoesnt really).
FACTOID
Reference
WIKITEXT
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Wikitexts
WikiText are like one blockof text from a MediaWiki(what Wikipedia is basedon) page.
WIKITEXT
ATTACHMENT
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And thats it!
A startup guide will launch when youdownload and run the tool to orient youto things in more detail.
Also, there are highly-detailed tutorialsavailable in the Tutorial Wizard tool.
Happy cloning!