Posters :: CouchDB (Davis P, Kumar S)

If you submit a poster to the conference and would like to be included here, please contact the co-chairs with your poster details.

The following are confirmed poster presentations. Note that there is no dedicated poster session for the workshop – there is just one general poster session for the conference. The information below should help you to find the posters relevant to our workshop.

Lab2: a Web platform for mouse geneticists
Paul LF Tang, You-Qiang Song
Department of Biochemistry, The University of Hong Kong, Hong Kong, China

Communicating Results from International Collaborations in the Information Age: Introducing the Genomic Applications for Humanity (Genapha) Website
Denise Daley, D Zamar, J Park, B Tripp
James Hogg iCAPTURE Center, University of British Columbia, Vancouver, BC

Open Data and Apache CouchDB

Paul J Davis, S Kumar
New England Biolabs

Recent developments in next generation sequencing as well as the focus on high throughput techniques is creating a data deluge that can befuddle even experienced bioinformaticians. Here we will discuss the traditional infrastructure of RDBMS’s (Relational Database Management Systems), their limitations, and how CouchDB is poised to overcome them. Traditional data storage techniques utilizing RDBMS’s require that a structure is applied to the stored data. The assumption of an a priori schema has long been an impedance mismatch for many different data domains including biological data. CouchDB uses a schema-less JSON (JavaScript Object Notation) document system which provides a low impedance mismatch with biological data. As data sizes grow, RDBMS’s typically have great difficulty in scaling past a single physical node. Currently, most multi-node systems use a master-slave topology in which the master node is the single writer and each slave is a read only node. CouchDB utilizes MVCC (Multi-Version Concurrency Control) to provide non-blocking read/write operations as well as a consistent reader view of the database. Leveraging consistent reader views, peer-based replication allows CouchDB to incrementally synchronize geographically
distributed nodes while being robust in the face of network disconnections. Interacting with CouchDB is accomplished via a REST (Representation State Transfer) API via HTTP (Hypertext Transfer Protocol). As such, any computer language or other environment capable of retrieving web pages is already capable of communication with CouchDB. CouchDB is a member of the Apache Software Foundation.

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