Chapman_publishingweb_BOSC2009

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?

Chapman_publishingweb_BOSC2009

by bosc

Accessibility

Categories

Upload Details

Usage Rights

Statistics