Pathway Tools supports creation, editing, querying, visualization, and analysis of Pathway/Genome Databases, or PGDBs.

The software also allows users to publish a PGDB on the Web for access by the scientific community. More than 250 groups have applied Pathway Tools to analyze more than 2,500 genomes from all domains of life [list of external PGDBs].

Citation:

The software provider asks users to cite the following articles in publications resulting from the use of the Pathway Tools software, the EcoCyc or MetaCyc databases, or from the BioCyc collection as a whole.

For Pathway Tools please cite:

Karp, P.D., et al., "Pathway Tools version 13.0: Integrated Software for Pathway/Genome Informatics and Systems Biology", Briefings in Bioinformatics, 11:40-79 2010.

http://bib.oxfordjournals.org/cgi/content/abstract/bbp043.

For EcoCyc please cite:

Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., Peralta-Gil, M., Santos-Zavaleta, A., Shearer, A.G., and Karp, P.D., EcoCyc: A comprehensive view of Escherichia coli biology, Nucleic Acids Research 37:D464-D470 (2009)

For MetaCyc or BioCyc please cite:

Caspi, R., Altman, T., Dale, J.M., Dreher, K., Fulcher, C.A., Gilham, F., Kaipa, P., Karthikeyan, A.S., Kothari, A., Krummenacker, M., Latendresse, M., Mueller, L.A., Paley, S., Popescu, L., Pujar, A., Shearer, A., Zhang, P. and Karp, P.D. MetaCyc: The MetaCyc Database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases, Nucleic Acids Research 38:D473-D479, 2010.

Please send Pathway Tools bug reports or suggestions to ptools-support@ai.sri.com.

Installation:

To install on:

• CAS ITS-supported Dell PCs, Macs, and Linux desktop computers: Submit request to get software installed.