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
- 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