Team:Washington/tools/created/new-software

Software Tools

As the systems created by synthetic biologists get more complex, automation and computer-aided design will be needed. Computers will eventually play an important part in the design, construction, and testing of new devices. To meet the emerging needs of synthetic biology, the UW iGEM team has developed several new software tools.

TinkerCell

[http://www.tinkercell.com TinkerCell] is being developed by [http://openwetware.org/wiki/User:Deepak_Chandran Deepak Chandran] as part of his PhD work with the [http://www.sys-bio.org/ Sauro Lab]. It can be used to design and model genetic networks and other complex sets of reactions. Eventually, it will retrieve a list of available parts from sources like the [http://www.partsregistry.org/Main_Page Parts Registry], but for now generic parts must be added and their parameters specified manually.

WikiDust

WikiDust is a plugin for TinkerCell that can be used to export models to the iGEM wiki or other webpages. Other users can then download the models for use in their own larger system, or to see how they responed when parameters are changed.

The first thing WikiDust does is allow you to associate TinkerCell items with parts on the registry. It's easy to use: 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.

After you've linked all the parts in your device or system to their associated wiki pages, you can upload a representation of it to your page.

Batch Part Submitter

The UW team will also develop a program to submit multiple parts at once based on a spreadsheet. 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.

This will be a simple command-line tool. The user will make a spreadsheet with information about all the parts to be submitted. Then our tool will validate and submit each one to the registry.

Code Testing Area

Just ignore anything in here...