About Pathway Tools
Pathway Tools is a comprehensive symbolic systems biology software system that supports several use cases in bioinformatics and systems biology:
- Development of organism-specific databases called Pathway/Genome Databases (PGDBs) that integrate many bioinformatics datatypes, from genomes to pathways to regulatory networks.
- Development of metabolic-flux models using flux-balance analysis
- Scientific visualization, web publishing, and dissemination of those organism-specific databases, including:
- Automatic display of metabolic pathways and full metabolic networks; generation of metabolic map diagram and of metabolic map poster (example).
- Genome browser; comparative genome browser; generation of genome poster (example).
- Display of operons, regulons, and full transcriptional regulatory networks
- Analysis of omics datasets, including painting omics data on to diagrams of the full metabolic network, enrichment analysis.
- Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, prediction of operons
- Comparative analyses of model-organism databases.
- Analysis of biological networks:
- Interactively tracing metabolites through the metabolic network
- Finding dead-end metabolites in metabolic networks
- Identifying choke points (potential drug targets) in metabolic networks
Pathway Tools has four 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 the BioCyc web site at BioCyc.org.
- MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases.
- Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.
Visit the Pathway Tools website.
- Download Pathway Tools: http://biocyc.org/download.shtml
- Source code is available on execution of software license.
Using Pathway Tools
Start with an annotated genome in the form of a Genbank file; Pathway Tools will do the rest.
Documentation is available within the software distribution. For an overview of the tool, see Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology 
Publications, Tutorials, and Presentations
Publications on or mentioning Pathway Tools
- Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. 
- An advanced web query interface for biological databases. 
- The pathway tools pathway prediction algorithm. 
- Regulatory network operations in the Pathway Tools software. 
- Pathway Tools slides
- General information about Pathway Tools, including slides from tutorials and user guides
- Upcoming Events
- Pathway Tools tutorials and workshops
Contacts and Mailing Lists
|Mailing List Link||Description||Archive(s)|
|Pathway Toolsemail@example.com||Pathway Tools users list. To subscribe to this list, send a request to firstname.lastname@example.org.||None|
Pathway Tools in the wild
Pathway Tools Development
The Pathway Tools Developers' Corner has updates and information on current and proposed Pathway Tools developments.
See the samples section of the BioCyc website for details of the types of data that are stored in a PGDB.
More on Pathway Tools
- Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief. Bioinformatics 2010 11 40-79
- An advanced web query interface for biological databases. Database (Oxford) 2010 2010 baq006
- The pathway tools pathway prediction algorithm. Stand Genomic Sci 2011 5 424-9
- Regulatory network operations in the Pathway Tools software. BMC Bioinformatics 2012 13 243
Raw tool data at Pathway Tools/tool data