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Menlo Park, CA 94025-3493
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Pathway Tools is a systems biology software system that supports several use cases: development of organism-specific database that integrate many bioinformatics datatypes, from genomes to pathways; Development of metabolic-flux models using flux-balance analysis; scientific visualization, web publishing, and querying of organism-specific databases; analysis of omics datasets; and Computational prediction of metabolic pathways, metabolic pathway hole fillers, and operons.
The following are in reverse chronological order of publication.
Caspi R, Billington R, Ferrer L, Foerster H, Fulcher CA, Keseler IM, Kothari A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases.. Nucleic Acids Res, vol. 44, no. D1, pp. D471-D480, 2016. [Details]
Caspi R, Altman T, Billington R, Dreher K, Foerster H, Fulcher CA, Holland TA, Keseler IM, Kothari A, Kubo A, Krummenacker M, Latendresse M, Mueller LA, Ong Q, Paley S, Subhraveti P, Weaver DS, Weerasinghe D, Zhang P, Karp PD. The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res., vol. 42, no. 1, pp. D459-D471, 2014. [PDF, Details]