Biomedical research has become increasingly dependent upon software and visualization tools to analyze gene and protein sequences. Providing a proper information technology support environment to analyze sequences and store the data produced is essential, but often presents a particular challenge to researchers who have conducting """"""""wet lab"""""""" investigations as their main goal. At present, 28,000 researchers and students depend on the Biology Workbench (workbench.sdsc.edu) to meet their needs for sequence analysis software, data storage, and data retrieval. The Biology Workbench provides users free access to web-based environment where users with only an internet browser can conduct analyses, access databases, and store their results. Users have access to 80 sequence analysis functions and 33 remote databases of international significance, and a storage allocation for their personal data. The user base of the Biology Workbench has now grown larger than the original architecture of the Biology Workbench can support, and its rate of growth remains constant. This proposal outlines a methodology to refractor the existing Biology Workbench to create a more modular, more stable platform to meet the needs of Molecular Biologists for analytical tools, databases, and an area to store the results of their work. In its refactored form, the Next Generation Biology Workbench created under this funding will remove the limitation on number of users, create an easily expansible, reusable structure into which community codes can be mounted. It will provide users access to all currently available Workbench tools, and a variety of new enabling technologies, including visualization tools, Web Services, a user configurable interface, peer-to-peer data sharing capabilities, and grid computing capabilities. The proposal outlines a well defined methodology for creating and evolving the software created under this proposal to ensure that it meets the needs of its user base. It also describes a methodology for expanding the user base into new communities.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM073931-02
Application #
7037447
Study Section
Special Emphasis Panel (ZRG1-MABS (01))
Program Officer
Whitmarsh, John
Project Start
2005-04-01
Project End
2009-03-31
Budget Start
2006-04-01
Budget End
2007-03-31
Support Year
2
Fiscal Year
2006
Total Cost
$518,380
Indirect Cost
Name
University of California San Diego
Department
Biostatistics & Other Math Sci
Type
Schools of Arts and Sciences
DUNS #
804355790
City
La Jolla
State
CA
Country
United States
Zip Code
92093
Miller, Mark A; Schwartz, Terri; Pickett, Brett E et al. (2015) A RESTful API for Access to Phylogenetic Tools via the CIPRES Science Gateway. Evol Bioinform Online 11:43-8