Team:Washington/Tools Created/New Software

As the systems created by synthetic biologists get more complex, automation and computer-aided design will be needed. Computers will eventually have a central part to play in the design, construction, and testing of new devices. To meet the emerging needs of the synthetic biology community, the Washington 2010 iGEM team has developed two new software tools.

WikiDust is a plugin for TinkerCell. It can be used to export 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. WikiDust will provide an easy way to share models, encouraging more teams and researchers to describe their parts quantitatively. This in turn will help others reuse of their parts in the future.

The first thing WikiDust does is allow you to associate TinkerCell items with parts on the registry. The same mechanism could also be extended in the future to download the reaction kinetics, icon, etc. of the items into TinkerCell. For now though, it demonstrates the feasability of using a publicly available semantic knowledgebase to retrieve part information.

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.

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 your page. 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. Clicking an item in the uploaded diagram will go to the correct part page. In fact, our Tse2/Tsi2 diagram was generated using WikiDust.

To start using WikiDust, just download TinkerCell. It will automatically keep you up to date with the latest version.

We have also developed a command-line tool to submit multiple parts to the Registry at once. This will make it much easier and faster to submit a series of similar parts—promoters of different strengths, variations on a protein, etc. We used it to submit most of our parts.

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 program will log into the Registry and check your parts for syntax errors. Then, after you give the go-ahead, it will submit them.

Get PartsRobot from the SourceForge page.