Pathway Tools

As comprehensive symbolic systems biology software system, Pathway Tools is used by research groups to create pathway databases for organisms with sequenced genomes. Hundreds of pathway databases share a common schema, which facilitates data sharing and comparative analyses.

More than 3,000 academic and commercial groups have licensed SRI's Pathway Tools software to access existing databases. Licenses are available at no charge to research organizations.

Pathway Tools supports several use cases in bioinformatics and systems biology, including:

• Development of organism-specific databases (also called model-organism databases) that integrate many bioinformatics datatypes, from genomes to pathways.

• Scientific visualization, web publishing, and dissemination of those organism-specific databases, including:

  • Automatic display of metabolic pathways and full metabolic networks

  • A genome browser

  • Display of operons, regulons, and full transcriptional regulatory networks

• Visual analysis of omics datasets, such as painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome

• Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons

• Development of quantitative metabolic flux models using the method of flux-balance analysis

• Comparative analyses of organism-specific databases

Pathway Tools provides a powerful and comprehensive set of features for querying, visualization, analysis, and curation of Pathway Genome Database, or PGDBs. PGDBs are bioinformatics databases that integrate genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signaling pathways, and of the regulatory network. The software also allows users to publish a PGDB on the web for querying by the scientific community.

Pathway Tools has four software components:

• PathoLogic: Creates a new PGDB containing the predicted metabolic pathways of an organism, given a Genbank entry as input.

• Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers SRI’s BioCyc website.

• MetaFlux: Accelerates development of flux-balance analysis models

• Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.

Pathway Tools was developed by the Bioinformatics Research Group in SRI’s Artificial Intelligence Center. Development has been funded by grants from the National Institutes of Health (NIH).