Team:Washington/tools/created/new-software

Initial Motivation

Currently, there are many parts in the [http://www.partsregistry.org Parts Registry], but most of them are not well-described. This makes finding parts compatible with a given input or output, or that perform a certain function, difficult. Our project aims to provide guidelines for the "minimum useful information" that must accompany a part in order for it to be easily reused by other iGEM teams and researchers, and to make describing a part according to those guidelines as simple (and inviting) as possible.

The first stage of the project is to describe various types of BioBricks: oscillators, switches, reporters etc. These descriptions will include diagrams, a short description, a quantitative and/or mathematical model of how the part functions (when available), as well as other information. Much of this will be based on the description of [http://partsregistry.org/Part:BBa_F2620 BBa_F2620] provided by [http://www.ncbi.nlm.nih.gov/pubmed/18612302?itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum&ordinalpos=1 Canton et al 2008].

Once common themes start to emerge in how different parts can be described, the next stage will be to develop guidelines. What must be included with a part when it is submitted to the Registry, and what should be recommended, but not required?

Finally, a system will be set up to help people submit information about their parts to the Registry. This may take the form of a script or webpage, or even a complete program.

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...