Team:Washington/Tools Created/New Software

From 2010.igem.org

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(Part Submission Made Easy)
(Part Submission Made Easy)
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[[Image:uw_sauro_submitter_mockup.png|600px|right]]
[[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 something like:
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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:
<code>python partsrobot.py submit yourspreadsheet.csv </code>
<code>python partsrobot.py submit yourspreadsheet.csv </code>
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(Your exact command will vary with operating system, file locations, etc. See the instructions for details.)
+
(The exact command varies with operating system and file locations. For details see the instructions.)
Once launched, the program will log into the Registry and check your parts for syntax errors. Then, after you give the go-ahead, it will submit them. Most of [[Team:Washington/Parts|our parts]] were submitted this way.
Once launched, the program will log into the Registry and check your parts for syntax errors. Then, after you give the go-ahead, it will submit them. Most of [[Team:Washington/Parts|our parts]] were submitted this way.

Revision as of 17:31, 27 October 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 (BBF RFC 68), as well as two new software tools, WikiDust and PartsRobot.

Wikidust banner.png

A Standard for Electronic Diagrams

Distribution of standardized diagrams describing DNA construct designs for synthetic biology depends both on the use of a standard set of symbols and on the method of distribution. Therefore the two main requirements for our proposed standard, BBF RFC 68, are:

  1. The use of SBOLv symbols
  2. The linking of symbols to reference entry pages on the Registry of Standard Biological Parts using http URLs

The result constitutes a diagram which allows the reader to click on portions of the diagram which correspond to SBOLv symbols and read the reference information about that particular portion of the diagram.

Software to Create and Share Standards-Compliant Diagrams

WikiDust is a plugin for TinkerCell, a computer-aided design tool developed here at the 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 the 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 Standard Virtual Parts Repository or the Biomodels Database. For now though, it demonstrates the feasability of using the publicly available 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 representation 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 TinkerCell download page.


Partsrobot banner.png

Part Submission Made Easy

PartsRobot is a command-line tool that can submit many parts to the Registry at once. This makes it much easier and faster 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

(The exact command varies with operating system and file locations. For details see the instructions.)

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


Get PartsRobot from the SourceForge page.

New Vectors       Tools Used