open-source

Talking at BOSC 2009 about publishing biological data on the web

Brad Chapman bio photo By Brad Chapman Comment

The Bioinformatics Open Source Conference (BOSC) is taking place later this month in Stockholm, Sweden. I will be attending for the first time in a few years, and giving a short and sweet 10 minute talk about ideas for publishing biological data on the web. BOSC provides a chance to meet and talk with many of the great people involved in open source bioinformatics; the schedule this year looks fantastic. The talk will be held in conjunction with The Data and Analysis Management special interest group, also full of interesting talks.

The talk will promote development of reusable web based interface libraries layered on top of existing open source projects. The PDF abstract provides the full description and motivation; below is a more detailed outline based on some brainstorming and organization:

  • Motivation: rapidly organize and display biological data in a web accessible format.
  • Current state: reusable bioinformatics libraries targeted at programmers -- Biopython, bx-python, pygr, PyCogent
  • Current state: back end databases for storing biological data -- BioSQL, GMOD
  • Current state: full featured web applications targeted at users -- Galaxy, GBrowse
  • My situation: biologist and developer with organized data that needs analysis and presentation, internally with collaborators and externally with larger community.
  • Proposal: integrate bioinformatics libraries, database schemas, and open source web development frameworks to provide re-usable components that can serve as a base for custom data presentation.
  • Framework: utilize cloud infrastructure for reliable deployment -- Google App Engine, Amazon EC2
  • Framework: make use of front end javascript frameworks -- jQuery, ExtJS.
  • Framework: make use of back end web frameworks -- Pylons
  • Implementation: Demo server for displaying sequences plus annotations
  • Implementation: Utilizes BioSQL schema, ported to object oriented data store; Google App engine backend or MongoDB backend
  • Implementation: Data import/export with Biopython libraries -- GenBank in and GFF out
  • Implementation: Additional screenshots from internal web displays.
  • Challenges: Generalizing and organizing display and retrieval code without having to buy into a large framework.
  • Challenges: Re-usable components for cross-language functionality; javascript front end displays for multi-language back ends.
  • Challenges: Build a community that thinks of reusing and sharing display code as much as parsing and pipeline development code.

I would be happy to hear comments or suggestions about the talk. If you're going to BOSC and want to meet up, definitely drop me a line.

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