Available on platform
|
web +
, linux +
, os x +
, windows +
|
Date published
|
2010 +
, 2011 +
, 2012 +
|
Has DOI
|
10.1093/bib/bbp043 +
, 10.1093/database/baq006 +
, 10.4056/sigs.1794338 +
, 10.1186/1471-2105-13-243 +
|
Has PMCID
|
PMC2810111 +
, PMC2911841 +
, PMC3368424 +
, PMC3473263 +
|
Has PMID
|
19955237 +
, 20624715 +
, 22675592 +
, 22998532 +
|
Has URL
|
http://biocyc.org/download.shtml +
, http://bioinformatics.ai.sri.com/ptools/ +
, http://biocyc.org/ +
, http://biocyc.org/ECOLI/ +
, 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 +
, Caspi R +
|
Has description
|
list of PGDBs hosted elsewhere +
, 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 ([http://bioinformatics.ai.sri.com/posters/ecoli-metab.pdf example]).
**Genome browser; comparative genome browser; generation of genome poster ([http://bioinformatics.ai.sri.com/posters/ecoli-genome.pdf 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 status
|
active +
|
Has download URL
|
http://biocyc.org/download.shtml +
|
Has input format
|
Genbank format +
, GFF +
|
Has logo
|
PathwayTools.png +
|
Has output format
|
Genbank format +
, SBML +
, 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 +
, 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'' +
, 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 +
, wild URL +
|
Published in
|
Briefings in bioinformatics +
, Database : the journal of biological databases and curation +
, Standards in genomic sciences +
, 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 +
, Ontology Visualization +
|
Has improper value forThis property is a special property in this wiki.
|
Has title +
, Has description +
|
Categories |
Pathway Tools +
, GMOD Components +
, Tool data +
, GMOD Component +
, SemanticLink +
|
Modification dateThis property is a special property in this wiki.
|
16 October 2013 00:07:17 +
|
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/ +
, Pathway Tools#http://biocyc.org/otherpgdbs.shtml +
|