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Pathway Tools

Pathway Tools is an extensive bioinformatics software package that helps researchers model and analyze genomes, metabolic pathways, and regulatory networks. It works with the included BioCyc collection of 9,300 Pathway/Genome Databases (PGDBs) and on third-party PGDBs. The software also allows users to create new PGDBs and publish them on the web for querying by the scientific community.

Pathway Tools has been licensed to more than 7,000 academic and commercial groups to date. Licenses are available at no charge to research organizations and for a fee to commercial firms.

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  • Visualizations tailored to each of the following object types:
    • Biochemical pathways and reactions
    • Metabolites
    • Genes, proteins, and RNAs
    • Operons and regulatory interactions
  • Genome Browser that depicts genomic regions at user-selected resolution with semantic zooming that reveals new features at higher resolutions.  A tracks facility visually plots user data against the genome.
  • Development of quantitative metabolic flux models using flux-balance analysis.
  • Transcriptomics data analysis through visualization on a novel cellular dashboard, on a low-resolution depiction of an entire genome, on metabolic maps and individual pathways, and on regulatory network diagrams.
  • Metabolomics Data Analysis through visualization of metabolite sets on a novel cellular dashboard, on individual pathways and on the full metabolic map, and through metabolite enrichment analysis.
  • Comparative pathway and genome analyses

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). Visit the Pathway Tools website to learn more.

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