Short 10 minute talk encouraging bioinformatics programmers to organize and reuse code targeted at making data easily available on the web. Current open source technologies are combined into a higher level framework. An example implementation using Google App Engine and existing bioinformatics libraries is presented.

1. Lowering barriers to
publishing biological data on
the web
Brad Chapman
Department of Molecular Biology
Massachusetts General Hospital
Boston, MA USA
chapmanb@50mail.com
http://friendfeed.com/chapmanb
27 June 2009

2. Motivation

3. Motivation
Web accessible
Interoperable in standard formats
Displays for browsing
Analyses
Scale

4. Current state: Reusable libraries
Parse file formats
Run programs
Build analysis pipelines
Communities
Python examples
Biopython pygr
bx-python PyCogent

5. Current state: Database schemas
Represent biological data
Expand analyses beyond flat files
Interoperate with standards
BioSQL Chado

6. Current state: Web applications

7. Faster and Bigger

8. Proposal
Provide
Reusable presentation components
Quickly deployable frameworks
Integrate
Bioinformatics libraries
Database schemas
Web development frameworks

9. Proposal

10. http://biosqlweb.appspot.com/

11. Challenges: Design
Reusable
Components: avoid large framework
Multi-language: javascript front end
Accessible
Automated data retrieval (REST)
Standard formats (GFF, RDF)
Available
Creative Commons
http://creativecommons.org/about/licenses
Open Data Commons
http://www.opendatacommons.org/licenses/

12. Challenges: Community questions
How do we. . .
provide plug-in components?
leverage existing code?
make reuse easier?
communicate about these issues?