[画像:Pathway Tools logo]
Status
- Mature release
- Development: active
- Support: active
Resources
Facts about
"Pathway
Tools "
Available on platform
web
+ ,
linux
+ ,
os x
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and windows
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Has URL
http://biocyc.org/download.shtml
+ ,
http://bioinformatics.ai.sri.com/ptools/
+ ,
http://biocyc.org/
+ ,
http://biocyc.org/ECOLI/
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and http://biocyc.org/otherpgdbs.shtml
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Has description
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
(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.nteractive editing capabilities for PGDBs.
and list of PGDBs
hosted elsewhere
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