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Publication Details

The Pathway Tools Software

by Karp, P.D. and Paley, S. and Romero, P.

Bioinformatics, vol. 18, pp. S225-S232, 2002.

Abstract

Motivation: Bioinformatics requires reusable software tools for creating model-organism databases (MODs). Results: The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic network of an organism. This paper provides an overview of the four main components of the Pathway Tools: The PathoLogic component supports creation of new PGDBs from the annotated genome of an organism. The Pathway/Genome Navigator provides query, visualization, and Web-publishing services for PGDBs. The Pathway/Genome Editors support interactive updating of PGDBs. The Pathway Tools ontology defines the schema of PGDBs. The Pathway Tools makes use of the Ocelot object database system for data management services for PGDBs. The Pathway Tools has been used to build PGDBs for 13 organisms within SRI and by external users. Availability: The software is freely available to academics and is available for a fee to commercial institutions.

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Associated Projects

Pathway Tools

Pathway Tools

Pathway Tools is a systems biology software system that supports several use cases: Development of organism-specific database that integrate many bioinformatics datatypes, from genomes to pathways. Development of metabolic-flux models using flux-balance analysis. Scientific visualization, web publishing, and querying of organism-specific databases. Analysis of omics datasets. Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons. Comparative analyses.

AIC Personnel

Name Title E-mail
Karp, Peter D Director, Bioinformatics Research Group
Paley, Suzanne Computer Scientist
Romero, Pedro R Alumnus

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