Pathway Tools Software
Pathway Tools Software
Pathway Tools is a comprehensive symbolic systems biology software
system that is associated with the BioCyc database collection.
The software has been licensed by more than 9,000 groups and powers
a number of websites for biological databases.
Pathway Tools supports several use cases in bioinformatics and systems
- Development of organism-specific databases
(also called model-organism databases) that integrate many
bioinformatics datatypes, from genomes to regulatory networks to metabolic and signaling pathways.
- Metabolic reconstruction and modeling.
- Scientific visualization 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 gene-expression and metabolomics 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, that can be used for genome analysis.
- 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 has Four Components
- PathoLogic: Creates a new Pathway/Genome Database (PGDB) containing the predicted metabolic pathways
and operons of an organism, given a Genbank or GFF file as input.
- Pathway/Genome Navigator: Supports query, visualization, and analysis of PGDBs.
The Navigator powers the BioCyc web site at BioCyc.org.
- MetaFlux: Supports development 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
Research Group at SRI International.
Pathway Tools Availability
Pathway Tools is freely available to academics for research purposes, and is available for a
Pathway Tools Publications
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
- Contribute new comparative capabilities to Pathway Tools.
- Contribute metabolic engineering capabilities to Pathway Tools.
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 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
Pathway Tools User Group Meetings
Additional Pathway Tools Information
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 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.
To unsubscribe, send an email to with the word unsubscribe in the Subject.
The development of Pathway Tools is funded by grants GM077678,
GM080746, and GM75742 from the National Institutes of Health.