GMOD
Pathway Tools
Status
- Mature release
- Development: active
- Support: active
Resources
Facts about “Pathway Tools”
web +, linux +, os x + and windows +
http://biocyc.org/download.shtml +, http://bioinformatics.ai.sri.com/ptools/ +, http://biocyc.org/ +, http://biocyc.org/ECOLI/ + and http://biocyc.org/otherpgdbs.shtml +
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 +