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Publication Details

Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology.

by Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R.

Brief Bioinform., vol. 11, no. 1, pp. 40-79, Jan 2010.


Pathway Tools is a production-quality software environment for creating a type of model-organism database called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers and prediction of operons. It enables interactive editing of PGDBs by DB curators. It supports web publishing of PGDBs, and provides a large number of query and visualization tools. The software also supports comparative analyses of PGDBs, and provides several systems biology analyses of PGDBs including reachability analysis of metabolic networks, and interactive tracing of metabolites through a metabolic network. More than 800 PGDBs have been created using Pathway Tools by scientists around the world, many of which are curated DBs for important model organisms. Those PGDBs can be exchanged using a peer-to-peer DB sharing system called the PGDB Registry.

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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; and Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons.

AIC Personnel

Name Title E-mail
Altman, Tomer Scientific Application Programmer
Caspi, Ron MetaCyc Curator
Gilham, Fred Alumnus
Karp, Peter D Director, Bioinformatics Research Group
Keseler, Ingrid M Senior Scientific Database Curator
Krummenacker, Markus Bioinformatics Scientist
Latendresse, Mario Computer Scientist
Lee, Tom J Senior Research Engineer
Paley, Suzanne Computer Scientist
Spaulding, Aaron Computer Scientist
Subhraveti, Pallavi Scientific Programmer

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