clotho for users

8/3/2019 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 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!

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