Pathway Tools
From GMOD
Revision as of 18:42, 25 January 2007 by 165.124.152.78 (Talk)
- Description
- The Pathway Tools software is a bioinformatics software system for pathway analysis of genomes, and for creating Pathway/Genome Databases (PGDBs). A pathway/genome database (PGDB), such as EcoCyc, is a bioinformatics DB that integrates genomic data with detailed functional annotations of the genome, such as descriptions of metabolic and signaling pathways. A PGDB is a type of model-organism DB.
Pathway Tools supports extensive functionality including prediction, interactive editing, querying, and visualization of metabolic pathways and related datatypes including reactions, metabolites, and enzymes. It also includes query, visualization, and editing support for operons, genes, proteins, and chromosomes.
Pathway Tools can be coupled with other genome browsers to add support for pathways to an existing MOD.
Pathway Tools was developed by Peter D. Karp and coworkers at the Bioinformatics Research Group at SRI International.
- Demo & Screenshots
- See Samples
- Requirements
- Sun workstation, Windows2000 or XP, or Linux.
- Documentation
- See the Pathway Tools Information Site for links.
- Contact
- ptools-support@ai.sri.com.
- Downloads
- biocyc.org
Facts about "Pathway Tools"RDF feed
Available on platform | web +, linux +, os x + and windows + |
Date published | 2010 +, 2011 + and 2012 + |
Has DOI | 10.1093/bib/bbp043 +, 10.1093/database/baq006 +, 10.4056/sigs.1794338 + and 10.1186/1471-2105-13-243 + |
Has PMCID | PMC2810111 +, PMC2911841 +, PMC3368424 + and PMC3473263 + |
Has PMID | 19955237 +, 20624715 +, 22675592 + and 22998532 + |
Has URL | http://biocyc.org/download.shtml +, http://bioinformatics.ai.sri.com/ptools/ +, http://biocyc.org/ +, http://biocyc.org/ECOLI/ + and http://biocyc.org/otherpgdbs.shtml + |
Has author | Karp 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 description | list 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:
Pathway Tools has four components:
|
Has development status | active + |
Has download URL | http://biocyc.org/download.shtml + |
Has input format | Genbank format + and GFF + |
Has logo | PathwayTools.png + |
Has output format | Genbank format +, SBML + and BioPAX + |
Has publication details | Briefings 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 status | mature + |
Has support status | active + |
Has title | 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. +, E. coli PGDB + and Other PGDBs + |
Has topic | Pathway Tools + |
Has website | http://bioinformatics.ai.sri.com/ptools/ + |
Is open source | Caveats apply + |
Link type | download +, website +, public server + and wild URL + |
Published in | Briefings in bioinformatics +, Database : the journal of biological databases and curation +, Standards in genomic sciences + and BMC bioinformatics + |
Release date | 1999 + |
Tool functionality or classification | Community 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 + |