Web as platform: Wikified structure resources

October 3, 2008

topsanlogoThe bbgm wiki is run on Mindtouch Deki, which seems to be doing a pretty good job of making a business on top of their open source platform.

Earlier this year I had a chance to visit the New Communication Channels in Biology workshop in San Diego, where I found that Deki has quite a presence in the San Diego structural biology space, powering Topsan among other sites. The Mindtouch blog is carrying an interview with Srikrishna Subramanian, whom I had a chance to meet at Scifoo 2007. Definitely very curious about how the whole wiki-based approach to structural biology platform is going.

At the workshop I got the sense that they would like more crowdsourced involvement. Topsan does have an advantage, it’s related to the Protein Structure Initiative, and that’s where the early involvement should come. I think there needs to be a concerted effort (maybe there has been) to get everyone involved with the PSI to become active contributors, but that should only be the start. There are a whole bunch of people using PSI structures to generate structure-function information. They should get involved as well. I think if the structural biology community can start using Topsan as a key resource, then they’ll be in good shape. Perhaps it’s already there.

The interesting part for me will be to see how Topsan leverages Deki as more than just a wiki (which the interview alludes to). It’s a true web services platform and there could be some very innovative stuff done to make Topsan a true resource, not just another wiki, but a platform for structure-function information

Posted by Deepak Singh | Filed Under Informatics, Life Science, Web as platform 

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    As far as I know, Topsan includes proteins solved only by one (JCSG) structural genomics center. Honestly I doubt they will become the main resource for community structure annotation - there's too much artificial ownership of the data (crystallography is completely different in this respect from genomics).

    Of course it would be great to have a central place for such initiative, but it looks like NCBI-level institutions would be in position to create one.
 

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