Browsing metabolic and regulatory networks with BioCyc

Methods in Molecular Biology

Volumn 804, Issue , 2012, Pages 197-216

  Latendresse, Mario ^a   Paley, Suzanne ^a   Karp, Peter D ^a  

^a SRI INTERNATIONAL   (United States)

Author keywords

Browsing; Cellular network; Genome database; Highlighting; Metabolic database; Metabolic network; Regulatory network; Regulatory subnetwork; Web interface

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER PROGRAM; ESCHERICHIA COLI K 12; GENE REGULATORY NETWORK; GENETIC DATABASE; GENETICS; INTERNET; METABOLISM; METHODOLOGY;

COMPUTATIONAL BIOLOGY; DATABASES, GENETIC; ESCHERICHIA COLI K12; GENE REGULATORY NETWORKS; INTERNET; METABOLIC NETWORKS AND PATHWAYS; SOFTWARE;

ESCHERICHIA COLI;

EID: 84855882668     PISSN: 10643745     EISSN: None     Source Type: Book Series    
DOI: 10.1007/978-1-61779-361-5_11     Document Type: Article

References (8)

1. Caspi R, Altman T, Dale J, Dreher K, Fulcher C, Gilham F, Kaipa P, Karthikeyan A, Kothari A, Krummenacker M, Latendresse M, Mueller L, Paley S, Popescu L, Pujar A, Shearer A, Zhang P, Karp P. (2010) The Meta-Cyc database of metabolic pathways and enzymes and the BioCyc collection of Pathway/Genome Databases. Nucleic Acids Res, 38. (Database Issue): D473-D479.
2. BioCyc Database Collection. [http://BioCyc.org/otherpgdbs.shtml].
3. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, Amin N, Schwikowski B, Ideker T. (2003) Cytoscape: A software environment for integrated models of biomolecular interaction networks. Genome Res, 13 (11):2498-2504. (Pubitemid 37428274)
4. Karp P, Paley S, Krummenacker M, Latendresse M, Dale J, Lee T, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler I, Caspi R. (2009) Pathway Tools version 13.0: Integrated software for pathway/genome informatics and systems biology. Brief Bioinformn, 11(1):40-79.
5. Keseler I, Bonavides-Martinez C, Collado-Vides J, Gama-Castro S, Gunsalus R, Johnson DA, Krummenacker M, Nolan L, Paley S, Paulsen I, Peralta-Gil M, Santos-Zavaleta A, Shearer A, Karp P. (2009) EcoCyc: A comprehensive view of E. coli biology. Nucleic Acids Res, 37: D464-D470.
6. BioCyc Webinars. [http://biocyc.org/webinar.shtml].
7. BioCyc Downloads. [http://biocyc.org/download.shtml].
8. Comparison of BioCyc Desktop Mode and Web Mode. [http://biocyc.org/ desktop-vsweb-mode.shtml].