Robust Software Components for Model Organism Databases

Sri International, Menlo Park CA

Investigators

Linked publications & trials

Abstract

DESCRIPTION (provided by applicant): We propose to develop a set of robust software components for constructing model-organism databases (MODs). Those software components will support three main types of operations: creation of new MODs, interactive editing and curation of MODs, and Web publishing of MODs. Those three 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. The Pathway Tools is a mature, sophisticated, production-quality software environment. We further propose to provide support services for the growing user community for the Pathway Tools, to maintain quality documentation for the software, and to create two 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. Although Pathway Tools is particularly well adapted to microbial MODs, one goal of this application is to adapt the metabolic pathway part of Pathway Tools to work with MODs for higher organisms.