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Cyclone : Java-based querying and computing with Pathway Genome Databases
Le Fevre F, Smidtas S, Schachter V.
Bioinformatics, accepted 2007.

Querying and computing with BioCyc databases
Krummenacker M, Paley S, Mueller L, Yan T, Karp PD.
Bioinformatics. 15;21(16):3454-5. 2005.

BioWarehouse: a bioinformatics database warehouse toolkit.
Lee TJ, Pouliot Y, Wagner V, Gupta P, Stringer-Calvert DW, Tenenbaum JD, Karp PD.
BMC Bioinformatics. 2006 Mar 23;7:170.

Ongoing development of Cyclone
Le Fevre F, Smidtas S, Schachter V.
Pathway Tools User Group Meeting, Geneva, Switzerland. December 1, 2005 (pdf)

and also

The E. coli EcoCyc Database: No Longer Just a Metabolic Pathway Database
Karp P.D., Arnaud M., Collado-Vides J., Ingraham J., Paulsen I.T., Saier M.H. Jr.
ASM News 70(1): 25-30. 2004.

MetaCyc: a multiorganism database of metabolic pathways and enzymes
Cynthia J. Krieger, and Peter D. Karp
Nucleic Acids Research, 32(1):D438-42 2004.

The Pathway Tools Software
P. Karp, S. Paley, and P. Romero,
Bioinformatics 18:S225-32 2002.

Evaluation of computational metabolic-pathway predictions for H. pylori
S. Paley and P. Karp
Bioinformatics 18(5):705-14 2002.

The Generic Frame Protocol
P. D. Karp, K. Myers, and T. Gruber,
in Proceedings of the 1995 International Joint Conference on Artificial Intelligence, pp. 768--774, 1995.

Cytoscape: a software environment for integrated models of biomolecular interaction networks.
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T.
Genome Res. 2003 Nov;13(11):2498-504.

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