Collaborator: SRI International (Pathway Tools, BioCyc, MetaCyc)

Project Summary

Gramene's Cyc Pathways portal hosts 03 reference databases EcoCyc, PlantCyc and MetaCyc and 10 species-specific plant metabolic networks based on Pathway Tools platform developed by SRI International. 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.
  • 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
  • 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

    Principal Investigators

    Dr Peter D. Karp

    Director, Bioinformatics Research Group Artificial Intelligence Center, SRI International


  • Karp PD, Paley S, and Altman T. (2013). Data mining in the MetaCyc family of pathway databases.Methods Mol. Biol. 939:183-200. doi: 10.1007/978-1-62703-107-3_12.
  • Karp PD, Latendresse M, and Caspi R (2011). The pathway tools pathway prediction algorithm. Stand Genomic Sci. doi: 10.4056/sigs.1794338. link
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