Pathway Tools

From GMOD
Jump to: navigation, search



Pathway Tools logo
Status
  • Mature release
  • Development: active
  • Support: active
Resources


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.


Downloads



Using Pathway Tools

Start with an annotated genome in the form of a Genbank file; Pathway Tools will do the rest.


Documentation

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]

Publications, Tutorials, and Presentations

Publications on or mentioning Pathway Tools

  • 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]

Tutorials

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 Tools ptools-users@ai.sri.com Pathway Tools users list. To subscribe to this list, send a request to ptools-support@ai.sri.com. None

Pathway Tools in the wild

Public installations of Pathway Tools: 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.

Pathway Tools Development

Development team

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

Current status

The Pathway Tools Developers' Corner has updates and information on current and proposed Pathway Tools developments.

See also

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

See Category:Pathway Tools



  1. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:19955237
  2. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:20624715
  3. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:22675592
  4. Cite error: Invalid <ref> tag; no text was provided for refs named PMID:22998532

Raw tool data at Pathway Tools/tool data

Facts about "Pathway Tools"RDF feed
Available on platformweb +, linux +, os x + and windows +
Date published2010 +, 2011 + and 2012 +
Has DOI10.1093/bib/bbp043 +, 10.1093/database/baq006 +, 10.4056/sigs.1794338 + and 10.1186/1471-2105-13-243 +
Has PMCIDPMC2810111 +, PMC2911841 +, PMC3368424 + and PMC3473263 +
Has PMID19955237 +, 20624715 +, 22675592 + and 22998532 +
Has URLhttp://biocyc.org/download.shtml +, http://bioinformatics.ai.sri.com/ptools/ +, http://biocyc.org/ +, http://biocyc.org/ECOLI/ + and http://biocyc.org/otherpgdbs.shtml +
Has authorKarp PD +, Paley SM +, Krummenacker M +, Latendresse M +, Dale JM +, Lee TJ +, Kaipa P +, Gilham F +, Spaulding A +, Popescu L +, Altman T +, Paulsen I +, Keseler IM + and Caspi R +
Has descriptionlist of PGDBs hosted elsewhere + and Pathway Tools is a comprehensive symbolic 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.nteractive editing capabilities for PGDBs. +
Has development statusactive +
Has download URLhttp://biocyc.org/download.shtml +
Has input formatGenbank format + and GFF +
Has logoPathwayTools.png +
Has output formatGenbank format +, SBML + and BioPAX +
Has publication detailsBriefings in bioinformatics 11: 40-79 +, Database : the journal of biological databases and curation 2010: baq006 +, Standards in genomic sciences 5: 424-9 + and BMC bioinformatics 13: 243 +
Has software maturity statusmature +
Has support statusactive +
Has titlePathway 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. +, E. coli PGDB + and Other PGDBs +
Has topicPathway Tools +
Has websitehttp://bioinformatics.ai.sri.com/ptools/ +
Is open sourceCaveats apply +
Link typedownload +, website +, public server + and wild URL +
Published inBriefings in bioinformatics +, Database : the journal of biological databases and curation +, Standards in genomic sciences + and BMC bioinformatics +
Release date1999 +
Tool functionality or classificationCommunity Annotation +, Comparative Genome Visualization +, Database schema +, Database tools +, Gene Expression Visualization +, Genome Visualization & Editing +, Molecular Pathway Visualization + and Ontology Visualization +
Has subobjectThis property is a special property in this wiki.Pathway Tools#http://biocyc.org/download.shtml +, Pathway Tools#http://bioinformatics.ai.sri.com/ptools/ +, Pathway Tools#http://biocyc.org/ +, Pathway Tools#http://biocyc.org/ECOLI/ + and Pathway Tools#http://biocyc.org/otherpgdbs.shtml +