Pathway Tools Software

• Develop organism-specific databases that integrate many bioinformatics datatypes, from genomes to regulatory networks to metabolic and signaling pathways.

• Computational inferences including metabolic reconstruction and operon prediction.

• Scientific visualization and dissemination of those organism-specific databases via a public or private website:
  • Multiple search tools
  • Information pages for genes, metabolic pathways, reactions, and metabolites
  • A genome browser, metabolic network browser, and regulatory network browser

• Analysis suite for gene-expression and metabolomics data.

• Development of quantitative metabolic models.

• Comparative genome and pathway analyses.

• Analysis of biological networks:
  • Search for routes between specified metabolites
  • Find dead-end metabolites
  • Identify choke points (potential drug targets) in metabolic networks

For a comprehensive summary of the Pathway Tools capabilities click here.

More Information

• Pathway Tools demonstration videos

• Pathway Tools overview publication

• Pathway Tools and BioCyc publications Page

• FAQ for Pathway Tools users

• System requirements

Pathway Tools Licensing

Pathway Tools is freely available to academics for research purposes, and is available for a

Contributions to Pathway Tools

• Development of the PerlCyc Perl API to Pathway Tools by Lukas Mueller of Boyce Thompson Institute
• Development of the JavaCyc Java API to Pathway Tools by the TAIR project
• Development of the RCyc API for the R Project by Tomer Altman of Stanford University
• Development of the SBML output module by Jeremy Zucker of the Broad Institute

Additional Information

• License Pathway Tools for download and installation

• Pathway Tools Blog

• Pathway Tools Desktop mode vs Web mode

• Release Note History -- Describes new features in past releases of Pathway Tools

• Curator's Guide for Pathway/Genome Databases

• Submit a bug report for Pathway Tools

• Write queries to Pathway/Genome DBs:
  • Using the Python, Java, Perl, and Lisp APIs
  • By querying flatfile dabases

• Installing patches for the Pathway Tools

• Ontologies used within Pathway Tools
  • Evidence Ontology
    • HTML form of the evidence ontology
    • Paper describing the evidence ontology: "An Evidence Ontology for use in Pathway/Genome Databases," Pacific Symposium on Biocomputing 9:190-201 2004.
  • Cell Component Ontology
    • HTML form of the Cell Component Ontology
  • Protein Features Ontology
    • HTML form of the protein-features ontology

• File formats
  • Input and output format: Sample Genbank format file
  • Input format: Sample PathoLogic format file
  • Input and output format: Sample GFF3 Format file
  • Input format: Sample PathoLogic genetic-elements.dat file
  • Output format: Flatfile format for Pathway/Genome DBs

• Operations
  • How to Copy a PGDB Between Computers
  • How to import a flat-file PGDB into Pathway Tools
  • Instructions for creating an Oracle Database for use with the Pathway Tools
  • How to logout after starting the web interface of Pathway Tools
  • Reference for GKB-Editor, the Pathway Tools frame and class hierarchy editor

• Tutorial slides
  • Tutorial slides by topic
  • Overview
  • Navigator
  • Metabolic Overview and Omics Viewer
  • The Pathway Tools schema
  • Editors
  • PathoLogic
  • Writing queries in Lisp, Perl, and Java
  • Administration

Contact Us

Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.

Subscribe to the Pathway Tools Mailing List: Mailing list members receive periodic news and updates about Pathway Tools, such as announcements regarding new releases of the software and databases. The mail volume tends to be less than 1 announcement per month.

To subscribe to the Pathway Tools mailing list, send an email to with the word subscribe in the Subject.

Funding Sources

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