Supporting the SBML layout extension

Bioinformatics

Volumn 22, Issue 23, 2006, Pages 2966-2967

  Deckard, Anastasia ^a   Bergmann, Frank T ^a   Sauro, Herbert M ^a  

^a KECK GRADUATE INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CHEMICAL MODEL; COMPUTER ANALYSIS; COMPUTER GRAPHICS; COMPUTER INTERFACE; COMPUTER MODEL; INFORMATION PROCESSING; INFORMATION PROCESSING DEVICE; INFORMATION SYSTEM; MOLECULAR MODEL; PRIORITY JOURNAL; SYSTEMS BIOLOGY;

EID: 33751376743     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btl520     Document Type: Article

References (9)

1. Elowitz,M.B. and Leibler,S. (2000) A synthetic oscillatory network of transcriptional regulators. Nature, 403, 335-338.
2. Fruchterman,T.M.J. and Reingold,E.M. (1991) Graph drawing by force-directed placement. Software, Practice and Experience, 21, 1129-1164.
3. Gauges,R. et al. (2006) A model diagram layout extension for SBML. Bioinformatics, 22, 1879-1885.
4. Hucka,M. et al. (2003) The systems biology markup language (SBML): A medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
5. Kholodenko,B.N. (2000) Negative feedback and ultrasensitivity can bring about oscillations, in the mitogen-activted protein kinase cascades. Eur. J. Biochem, 267, 1583-1588.
6. Kitano,H. (2005) Using process diagrams for the graphical representation of biological networks. Nat. Biotechnol., 23, 961-966.
7. Sauro,H.M. (2000) JARNAC: A system for interactive metabolic analysis. In Hofmeyr,J.-H.S., Rohwer,J.M. and Snoep,J.L. (eds), Animating the Cellular Map. Stellenbosch University Press, Stellenbosch, pp. 221-228.
8. Sauro,H. et al. (2003) Next generation simulation tools: The Systems Biology workbench and BioSPICE integration. OMICS, 7, 355-72.
9. Teusink,B. (2000) Can yeast glycolysis be understood in terms of in vitro kinetics of the constituent enzymes? Testing biochemistry. Eur. J. Biochem., 267, 5313-5329.