Team:Washington/Tools Created/New Software

WikiDust is a plugin that 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. We hope it will provide an easy way to share models, encouraging more teams and researchers to describe their parts quantitatively. This will allow successful reuse of their parts in the future.

The first thing WikiDust does is allow you to associate TinkerCell items with parts on the registry. When the TinkerCell model is uploaded to a webpage, clicking on each item will go to the correct part page--in fact, many of the interactive diagrams on this wiki will be generated using WikiDust. The same linking mechanism could also be extended in the future to set the reaction kinetics, icon, etc. of the items. For now though, it's mostly a proof of concept demonstrating the use of a new semantic knowledgebase of parts.

Associating a link with an item is easy: 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 the model of your device or system is finished, you can upload a representation of it to your page. WikiDust will automatically handle uploading to most [http://www.mediawiki.org/wiki/MediaWiki MediaWiki] sites, or it can just display code for you to copy and paste. By default, a download link for the complete model file is also included.

The UW team has also developed a program to submit multiple parts to the [http://partsregistry.org/Main_Page Parts Registry] at once. It will be useful for anyone who needs to submit a series of parts—promoters of different strengths, variations on a protein, etc.

Using PartsRobot is simple. Just fill out the template spreadsheet with information about each part. Then 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 it the go-ahead, it will submit them.

Download from the [http://sourceforge.net/p/partsrobot/home/ SourceForge page]!