Team:Washington/Tools Created/New Software

From 2010.igem.org

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</script></html>__NOTOC__As synthetic biologists create ever more complex systems, automation and computer-aided design are becoming indispensable. Computational tools will eventually play a central role in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the University of Washington 2010 iGEM team has developed a standard for the electronic distribution of diagrams, detailed in [[Team:Washington/Tools_Created/New_Software#A Standard for Electronic Diagrams|BBF RFC 68]]. We also created two new software tools: [[Team:Washington/Tools_Created/New_Software#wikidust|WikiDust]] and [[Team:Washington/Tools_Created/New_Software#partsrobot|PartsRobot]].
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__NOTOC__
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==[[Image:wikidust_banner.png|500px|center]]==
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WikiDust is a plugin that can be used to export [[Team:Washington/Project/Tools/Sauro/TinkerCell|TinkerCell]] models to the iGEM wiki or other webpages. Users can then download the models for use in their own larger system, or to see how they respond when parameters are changed. We hope it will provide an easy way to share models, encouraging more teams and researchers to describe their parts quantitatively. This will allow successful reuse of their parts in the future.
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===Update 11/30/2010:<br />This page will be locked soon, so be sure to visit the [http://www.tinkercell.com/plugins/wikidust WikiDust] and [http://sourceforge.net/p/partsrobot/home/ PartsRobot] sites for more current information.===
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==[[Image:wikidust_banner.png|500px|center]]==
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====<center>A Standard for Electronic Diagrams</center>====
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Standard, unambiguous diagrams are central to communication in many established fields of engineering, but have not yet been widely adopted by synthetic biologists. Through the use of diagrams based on SBOL-visual ([http://bbf.openwetware.org/RFC.html#BBF_RFC_16:_Synthetic_Biology_Open_Language_Visual_.28SBOLv.29_Specification BBF RFC 16]) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. Usefulness of shared diagrams depends both on a standard set of symbols and on the method of distribution. Therefore the two main requirements for our proposed standard, [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_68:_Standard_for_the_Electronic_Distribution_of_SBOLv_Diagrams BBF RFC 68], are:
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# The use of SBOLv symbols
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# The linking of symbols to reference entry pages on the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts] using http URLs
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In the resulting diagram, the reader can click on portions which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram. This makes research easier and promotes better part descriptions.
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The first thing WikiDust does is allow you to associate TinkerCell items with parts on the registry. When the TinkerCell model is uploaded to a webpage, clicking on each item will go to the correct part page--in fact, many of the interactive diagrams on this wiki will be generated using WikiDust. The same linking mechanism could also be extended in the future to set the reaction kinetics, icon, etc. of the items. For now though, it's mostly a proof of concept demonstrating the use of a new semantic knowledgebase of parts.
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====<center>Software to Create and Share Standards-Compliant Diagrams</center>====
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WikiDust is a plugin for [[Team:Washington/Tools Used/Software#tinkercell|TinkerCell]], a computer-aided design tool developed here at the [http://www.washington.edu/ University of Washington]. WikiDust can be used to export diagrams of TinkerCell models to the iGEM wiki or other webpages. Our goal in creating WikiDust is to provide an easy way to share models and to encourage iGEM teams and researchers to describe their parts more completely. This, in turn, will help others reuse them in future projects.
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[[Image:washington_rightclick.png|200px|left]][[Image:uw_sauro_linkpanel.png|300px|left]]
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Associating a link with an item is easy: just right click on an item and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one.
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One thing WikiDust does is provide a method to associate TinkerCell items, such as promoters or coding sequences, with parts on the Registry. The same mechanism could also be extended in the future to download reaction kinetics and other parameters from sources like the [http://www.ncbi.nlm.nih.gov/pubmed/20160009 Standard Virtual Parts Repository] or the [http://www.ncbi.nlm.nih.gov/pubmed/16381960 Biomodels Database]. For now though, it demonstrates the feasability of using the publicly available [http://www.sbolstandard.org Standard Biological Parts Knowledgebase (SBPkb)] to retrieve part information using Semantic Web standards.
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To associate a link with an item in TinkerCell, right click on it and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one. Click "Use Selected" to choose one from the list, or enter your own link and click "Use Custom".
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After the model of your device or system is finished, and you've added all the links you want, you can upload a diagram of it to a webpage. Just choose "Create Imagemap" from the TinkerCell plugins menu, and change any options you want in the window that pops up. WikiDust will automatically handle uploading to the iGEM wiki, or it can just display code for you to copy and paste to another site. The diagram will be interactive; clicking an item will take you to the correct part page. In fact, [https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram our tse2/tsi2 diagram] was generated using WikiDust.
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<!-- [[Image:uw_sauro_model_on_wiki.png|500px|left]] -->
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<!--[https://2010.igem.org/Team:Washington/Gram_Negative/Design#diagram https://static.igem.org/mediawiki/2010/4/44/Washington_Diagram_F2620_Tse2_Tsi2_2.png]-->
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After the model of your device or system is finished, you can upload a representation of it to your page. WikiDust will automatically handle uploading to most [http://www.mediawiki.org/wiki/MediaWiki MediaWiki] sites, or it can just display code for you to copy and paste. By default, a download link for the complete model file is also included.
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'''To start using WikiDust you’ll need the main TinkerCell program, as well as Python and Subversion. All three can be found on the [http://www.tinkercell.com/downloads-2 TinkerCell download page].'''
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==[[Image:partsrobot_banner.png|500px|center]]==
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====<center>Registry Submission Made Easy</center>====
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PartsRobot is a command-line tool that can submit many parts to the [http://partsregistry.org/Main_Page Registry] at once. This makes it fast and easy to enter information about a series of similar parts&mdash;promoters of different strengths, variations on a protein, etc.
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The UW team will also develop a program to submit multiple parts to the [http://partsregistry.org/Main_Page Parts Registry] at once. This project is in the early design phase now. It is expected to be useful for anyone who needs to submit a series of parts, for example if they are promoters of different strengths, variations on a protein, etc.
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[[Image:uw_sauro_submitter_mockup.png|600px|right]]
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Using PartsRobot is simple. Just fill out the template spreadsheet with information about each part. Then, in a command prompt, type:
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This will be a simple command-line tool. The user will make a spreadsheet with information about all the parts to be submitted. Then the tool will validate and submit each one to the registry.
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<code>python partsrobot.py submit yourspreadsheet.csv </code>
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Get PartsRobot at the [http://sourceforge.net/p/partsrobot/home/ SourceForge page]!
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(Exact command varies with OS and file locations. See the README for details.)
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Once launched, the program will log into the Registry and check your parts for syntax errors. After you give the go-ahead, it will submit them. Most of [[Team:Washington/Parts|our parts]] were submitted this way.
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'''You can download PartsRobot from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page].'''
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'''&larr; [[Team:Washington/Tools Created|Overview of Tools]]'''
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'''&larr; [[Team:Washington/Tools Created/New Vectors|New Vectors]]'''
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'''[[Team:Washington/Tools Used/Next-Gen Cloning|Next-Gen Cloning]] &rarr;'''
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'''[[Team:Washington/Tools Used|Overview of Tools We Used]] &rarr;'''
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{{Template:Team:Washington/Templates/Footer}}
{{Template:Team:Washington/Templates/Footer}}

Latest revision as of 17:31, 6 December 2010

As synthetic biologists create ever more complex systems, automation and computer-aided design are becoming indispensable. Computational tools will eventually play a central role in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the University of Washington 2010 iGEM team has developed a standard for the electronic distribution of diagrams, detailed in BBF RFC 68. We also created two new software tools: WikiDust and PartsRobot.

Update 11/30/2010:
This page will be locked soon, so be sure to visit the [http://www.tinkercell.com/plugins/wikidust WikiDust] and [http://sourceforge.net/p/partsrobot/home/ PartsRobot] sites for more current information.

Wikidust banner.png

A Standard for Electronic Diagrams

Standard, unambiguous diagrams are central to communication in many established fields of engineering, but have not yet been widely adopted by synthetic biologists. Through the use of diagrams based on SBOL-visual ([http://bbf.openwetware.org/RFC.html#BBF_RFC_16:_Synthetic_Biology_Open_Language_Visual_.28SBOLv.29_Specification BBF RFC 16]) symbols, we hope to facilitate communication about synthetic DNA constructs between research groups. Usefulness of shared diagrams depends both on a standard set of symbols and on the method of distribution. Therefore the two main requirements for our proposed standard, [http://openwetware.org/wiki/The_BioBricks_Foundation:RFC#BBF_RFC_68:_Standard_for_the_Electronic_Distribution_of_SBOLv_Diagrams BBF RFC 68], are:

  1. The use of SBOLv symbols
  2. The linking of symbols to reference entry pages on the [http://partsregistry.org/Main_Page Registry of Standard Biological Parts] using http URLs

In the resulting diagram, the reader can click on portions which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram. This makes research easier and promotes better part descriptions.

Software to Create and Share Standards-Compliant Diagrams

WikiDust is a plugin for TinkerCell, a computer-aided design tool developed here at the [http://www.washington.edu/ University of Washington]. WikiDust can be used to export diagrams of TinkerCell models to the iGEM wiki or other webpages. Our goal in creating WikiDust is to provide an easy way to share models and to encourage iGEM teams and researchers to describe their parts more completely. This, in turn, will help others reuse them in future projects.

Washington rightclick.png
Uw sauro linkpanel.png

One thing WikiDust does is provide a method to associate TinkerCell items, such as promoters or coding sequences, with parts on the Registry. The same mechanism could also be extended in the future to download reaction kinetics and other parameters from sources like the [http://www.ncbi.nlm.nih.gov/pubmed/20160009 Standard Virtual Parts Repository] or the [http://www.ncbi.nlm.nih.gov/pubmed/16381960 Biomodels Database]. For now though, it demonstrates the feasability of using the publicly available [http://www.sbolstandard.org Standard Biological Parts Knowledgebase (SBPkb)] to retrieve part information using Semantic Web standards.

Uw sauro mapprompt.png










To associate a link with an item in TinkerCell, right click on it and choose "Add Link". This will bring up a search window with suggested parts. You can search for a phrase, a BioBrick ID, etc. You can also open parts in a browser to read more about them or confirm that you've found the right one. Click "Use Selected" to choose one from the list, or enter your own link and click "Use Custom".

After the model of your device or system is finished, and you've added all the links you want, you can upload a diagram of it to a webpage. Just choose "Create Imagemap" from the TinkerCell plugins menu, and change any options you want in the window that pops up. WikiDust will automatically handle uploading to the iGEM wiki, or it can just display code for you to copy and paste to another site. The diagram will be interactive; clicking an item will take you to the correct part page. In fact, our tse2/tsi2 diagram was generated using WikiDust.


To start using WikiDust you’ll need the main TinkerCell program, as well as Python and Subversion. All three can be found on the [http://www.tinkercell.com/downloads-2 TinkerCell download page].


Partsrobot banner.png

Registry Submission Made Easy

PartsRobot is a command-line tool that can submit many parts to the [http://partsregistry.org/Main_Page Registry] at once. This makes it fast and easy to enter information about a series of similar parts—promoters of different strengths, variations on a protein, etc.

Uw sauro spreadsheet.png






















Uw sauro submitter mockup.png

Using PartsRobot is simple. Just fill out the template spreadsheet with information about each part. Then, in a command prompt, type:

python partsrobot.py submit yourspreadsheet.csv

(Exact command varies with OS and file locations. See the README for details.)

Once launched, the program will log into the Registry and check your parts for syntax errors. After you give the go-ahead, it will submit them. Most of our parts were submitted this way.


You can download PartsRobot from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page].

← New Vectors       Overview of Tools We Used →

Retrieved from "http://2010.igem.org/Team:Washington/Tools_Created/New_Software"