Pathway Tools/tool data
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 = 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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