GMOD

Pathway Tools/tool data

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

| 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 = http://bioinformatics.ai.sri.com/ptools/ | 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 BioCyc.org.
• MetaFlux: Supports development of metabolic flux models from Pathway/Genome Databases.
• Pathway/Genome Editors: Provide interactive editing capabilities for PGDBs.

| screenshot = | public_server = http://biocyc.org/ | dl = | dl_url = http://biocyc.org/download.shtml | 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	ptools-users@ai.sri.com	Pathway Tools users list. To subscribe to this list, send a request to ptools-support@ai.sri.com.	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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• Pathway Tools
• GMOD Components
• Tool data

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• Last updated at 18:32 on 10 September 2013.
• Content is available under a GNU Free Documentation License unless otherwise noted.