Pathway Tools/tool data

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This page contains the data that populates the Pathway Tools page.

{{ {{{template}}} | name = Pathway Tools | full_name = | status = mature | dev = active | support = active | type = Community Annotation, Comparative Genome Visualization , Database schema, Database tools, Gene Expression Visualization, Genome Visualization & Editing, Molecular Pathway Visualization, Ontology Visualization | platform = linux, os x, unix, win|platform = linux, os x, unix, win|platform = linux, os x, unix, win | platform = web | logo = PathwayTools.png | home = | about = 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
  • MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases.
  • Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.

| screenshot = | public_server = | dl = | dl_url = | dl_src = Source code is available on execution of software license. | dl_src_url = | dl_dev = | dl_dev_url = | getting_started_preamble = Start with an annotated genome in the form of a Genbank file; Pathway Tools will do the rest. | req = | install = | config = | doc = 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 [1] | papers =

  • Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. [1]
  • An advanced web query interface for biological databases. [2]
  • The pathway tools pathway prediction algorithm. [3]
  • Regulatory network operations in the Pathway Tools software. [4]

| presentations = | tutorials =

Pathway Tools slides
General information about Pathway Tools, including slides from tutorials and user guides
Upcoming Events
Pathway Tools tutorials and workshops

| wild_urls = There are a large number of PGDBs available via the BioCyc website, e.g. the E. coli PGDB, as well as a list of PGDBs hosted elsewhere. | mail =

Mailing List Link Description Archive(s)
Pathway Tools Pathway Tools users list. To subscribe to this list, send a request to None

| logo_info = | dev_ppl = Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International. | dev_status = The Pathway Tools Developers' Corner has updates and information on current and proposed Pathway Tools developments. | contact_email = Peter Karp | input = Genbank format; GFF | output = Genbank format; SBML; BioPAX | see_also = See the samples section of the BioCyc website for details of the types of data that are stored in a PGDB. | demo_server = | survey_link = Pathway_Tools |release date=1999 }}
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