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Pathway Tools
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 +
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