Lowering barriers to publishing biological data on the web (ISMB DAM/BOSC 2009)

Brad Chapman, biopython.org

Reusable libraries for parsing file formats, running programs, build analysis pipelines, etc are important. Python examples are biopython, pygr, etc. For representing biological data, BioSQL and Chado are examples of database schemas that represent biological data and help you move from flat files. We should integrate bioinformatics libraries, db schemas, and web development frameworks (among others).  An example implementation, deployed with Google App Engine, is at http://biosqlweb.appspot.com.

Challenges: how do we provide plug-in components, leverage existing code, make reuse easier, and communicate about these issues?

FriendFeed discussion:http: http://ff.im/4vtZi

Please note that this post is merely my notes on the presentation. They are not guaranteed to be correct, and unless explicitly stated are not my opinions. They do not reflect the opinions of my employers. Any errors you can happily assume to be mine and no-one else’s. I’m happy to correct any errors you may spot – just let me know!

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