| 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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