Pangea Systems proposes bioinformatics research aimed at further developing the EcoCyc database. EcoCyc is an electronic encyclopedia that is accessible to scientists through the World Wide Web, through a user-friendly graphical interface. It describes all known genes and all known metabolic pathways of E. coli. It serves as a general reference source for E. coli, and is particularly well suited for use in the analysis of microbial genomes. This project will add to EcoCyc detailed descriptions of other cellular processes within E. coli, such as regulation, transport, and macromolecule metabolism. EcoCyc will also become an up-to-date reference source on the evolving annotation of the full E. coli genome. This project will also develop a new database that describes metabolic pathways from a number of different microbes. This database will be useful to researchers who are annotating microbial genomes, and it will increase the power of a Pangea program that performs computational prediction of metabolic pathways in microbial genomes, called PathoLogic. This work will enhance the software capabilities of PathoLogic in a number of respects. The project will enhance the power of the GenoPath tools for querying and visualizing integrated collections of metabolic and genomic data; those tools form the software foundation for EcoCyc. EcoCyc is a reference source that is widely used by many scientists. When used as a basis for analyzing newly sequenced microbial genomes, EcoCyc contributes to the identification within those genomes of metabolic pathways that may serve as targets for drug design. Pharmaceutical companies are seeking targets within metabolic pathways as one strategy for developing next-generation drugs against antibiotic- resistant bacteria. The database is also useful for designing variants of biochemical pathways for biotechnology applications, and for teaching biochemistry.
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