SeToB stands for Schematic to Biobrick. It is the software project of University of Washington's 2008 iGEM team. The code repository is at: http://code.google.com/p/setob/.
The next step is to get features and subparts info into the pobol format. I have them parsed, but don't know how to show features on the format.
Then I plan to store about 20 PoBoLized Biobricks. Given say you want a repressor, it will show all the repressors (w/ promoters) available, and as you select that it will then show you what genes code for the repressor.
And underlying it will be using query language on PoBoL format BioBricks.
This looks great! Of course it's a little embarrassing (for our community) that you needed to fall back to screen-scraping, in first place... Can you modify your web server so that it directly returns the Pobol-formatted Biobrick when I ask for an address like: www.your.server.../parts#BBa_P1010 ? This way other tools (brickit in my case) could use your server as a spring board to fetch Pobol entries from the registry.
Concerning sequence features, Pobol indeed needs a way to describe them. My suggestion would be to first look at http://www.sequenceontology.org/ and see whether their terms and definitions can be linked into the pobol ontology. Any suggestions are very, very welcome. The pobol mailing list is the best place to discuss this. Good luck!
3 comments:
Awesome! Great to see it up and running! Congrats on getting the scraping going. What's the next step?
The next step is to get features and subparts info into the pobol format. I have them parsed, but don't know how to show features on the format.
Then I plan to store about 20 PoBoLized Biobricks. Given say you want a repressor, it will show all the repressors (w/ promoters) available, and as you select that it will then show you what genes code for the repressor.
And underlying it will be using query language on PoBoL format BioBricks.
This looks great! Of course it's a little embarrassing (for our community) that you needed to fall back to screen-scraping, in first place... Can you modify your web server so that it directly returns the Pobol-formatted Biobrick when I ask for an address like: www.your.server.../parts#BBa_P1010
? This way other tools (brickit in my case) could use your server as a spring board to fetch Pobol entries from the registry.
Concerning sequence features, Pobol indeed needs a way to describe them. My suggestion would be to first look at http://www.sequenceontology.org/ and see whether their terms and definitions can be linked into the pobol ontology. Any suggestions are very, very welcome. The pobol mailing list is the best place to discuss this. Good luck!
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