Pathway Tools Software (original) (raw)

Pathway Tools Software

Pathway Tools Bioinformatics Software

Pathway Tools is a comprehensive systems-biology software system that is associated with the BioCyc database collectionand supports several use cases in bioinformatics:

• Development of organism-specific databasesthat integrate many bioinformatics datatypes, including genomes, metabolic pathways, and regulatory networks.
• Metabolic reconstruction and metabolic-flux modeling using flux-balance analysis.
• Scientific visualization and web publishing 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
  • List of other websites powered by Pathway Tools
• Analysis of gene-expression, metabolomics, and multi-omics datasets, including pathway analysis and painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome.
• 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

Pathway Tools Components

• PathoLogic: Creates a new Pathway/Genome Database (PGDB) containing the predicted metabolic pathways of an organism, given a Genbank entry as input. Pathways are predicted from theMetaCyc pathway database.
• Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs. The Navigator powers the BioCyc web site at BioCyc.org.
• MetaFlux: Supports development and execution of metabolic flux models.
• Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.

Please see the Pathway Tools Overview document for more details on the capabilities of the software.

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

Pathway Tools Availability

Pathway Tools is freely available for research purposesto academic, non-profit, and government institutions, and is available for a

Pathway Tools Publications

• Overview publication on Pathway Tools
• See the BioCyc and Pathway Tools Publications Page

Contributions to Pathway Tools

We solicit contributions of new functionality to Pathway Tools. This is by no means an exclusive list, but rather a set of ideas for what might be contributed. Contributions can be integrated directly into the Pathway Tools build at SRI, or can be distributed separately by their authors for loading into Pathway Tools. Pathway Tools source code is available. Interested? Contact .

• Interface bioinformatics prediction algorithms to Pathway Tools so that predictions made by these tools can be integrated into a PGDB. Example predictors could include predictors of protein cellular location, or of regulatory elements.
• Contribute new comparative capabilities to Pathway Tools.
• Contribute metabolic engineering capabilities to Pathway Tools.

Past Contributors

We gratefully acknowledge the following contributions:

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

Pathway Tools User Group Meetings

• 2005 Meeting in Geneva
• 2006 Meeting at SRI International
• 2009 Meeting at SRI International
• 2010 Meeting at SRI International
• 2013 Meeting at SRI International

Additional Pathway Tools Information

• FAQ for Pathway Tools users
• Pathway Tools Blog
• License Pathway Tools for download and installation
• Release Note History -- Describes new features in past releases of Pathway Tools
• Pathway Tools Installation Guide (includes Solaris,linux and windows system requirements)
• Curator's Guide for Pathway/Genome Databases
• 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 format: Sample PathoLogic Format file
  • Input format: Sample PathoLogic genetic-elements.dat file
  • Input format: Sample .fba files
  • 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
  • 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

To report software bugs or for other questions, please contact us at .

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 is 1-2 announcements per month. To subscribe to the Pathway Tools mailing list, send an email to with the word subscribe in the Subject.

To unsubscribe, send an email to with the word unsubscribe in the Subject.

Funding Sources

The development of Pathway Tools is funded by grants R01AI160719 and 1R24GM150703 from the National Institutes of Health; and by grant NSF2109898 from the National Science Foundadtion.

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