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silenius

Pathway Tools Information Site


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 (also called model-organism databases) that integrate many bioinformatics datatypes, from genomes to pathways.
  • Scientific Visualization, web publishing, and dissemination of those organism-specific databases, including:
    • Automatic display of metabolic pathways and full metabolic networks
    • A genome browser
    • Display of operons, regulons, and full transcriptional regulatory networks
  • Visual analysis of omics datasets, such as painting omics data onto diagrams of the full metabolic network, full regulatory network, and full genome
  • Computational inferences including prediction of metabolic pathways, prediction of metabolic pathway hole fillers, and prediction of operons, that can be used for genome analysis
  • Comparative analyses of organism-specific 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
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