Team:Washington/tools/created/new-software

Software Tools

As the systems created by synthetic biologists get more complex, automation and computer-aided design will increasingly 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 types of complex 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.

Project Abstract

I will design a TinkerCell plugin that enables iGEM teams to embed TinkerCell modules and plots into their wiki pages to share with others. This will essentially use the CAD tool to generate 'data sheets' demonstrating the predicted behavior of a ‘device’. Experimental results will be optionally included for comparison. The nodes in TinkerCell generated diagrams, such as 'Parts', 'Proteins', and 'Small Molecules' will link to information pages describing that object, and pages that list other devices interacting with that molecule or Part.

Besides the core TinkerCell plugin, this would also ideally involve setting up a system for generating related wiki pages and writing a plugin that lets users add their experimental data to the modeled plots before exporting them to the wiki.

Also, I will create documentation for the proposed process of describing Devices. This will include a proposal for a minimal information standard (to be submitted as a [http://bbf.openwetware.org/RFC.html BBF RFC]) and an informal checklist to guide the workflow of reporting the characterization of 'Devices'.

Code Testing Area

Just ignore anything in here...