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

Batch Part Submitter

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...