Robust Software Components for Model Organism Databases

Sri International, Menlo Park CA

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Abstract

DESCRIPTION (provided by applicant): We propose to further develop a set of robust software components for constructing model-organism databases (MODs). Those software components will support 3 main types of operations: creation of new MODs, interactive editing and curation of MODs, and Web publishing of MODs. Those 3 types of operations will be supported for the following bioinformatics datatypes: genome maps, genes, operons, promoters, proteins, biochemical reactions, metabolic and signaling pathways, and small-molecule metabolites. These software components will be based on the Pathway Tools software that underlies the EcoCyc database, and other MODs. Pathway Tools is a mature, sophisticated, production-quality software environment that has been licensed by 60 groups who have constructed 20 existing MODs and plan to construct more than 20 additional MODs. We further propose to provide support services for the large and growing user community for the Pathway Tools, to maintain quality documentation for the software, and to create 2 thoroughly tested releases of the software per year. We will also interact with the community of developers of other MOD software components to ensure interoperability of our software components with components developed by other groups.