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

Motivation

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

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

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

Current state: Web applications

Faster and Bigger

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

Proposal

http://biosqlweb.appspot.com/

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/

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