Next Generation Simulation Tools: The Systems Biology Workbench and BioSPICE Integration

OMICS A Journal of Integrative Biology

Volumn 7, Issue 4, 2003, Pages 355-372

  Sauro, Herbert M ^a,b   Hucka, Michael ^b   Finney, Andrew ^b   Wellock, Cameron ^a   Bolouri, Hamid ^b,c   Doyle, John ^b   Kitano, Hiroaki ^d  

^a KECK GRADUATE INSTITUTE   (United States)

^b CALIFORNIA INSTITUTE OF TECHNOLOGY   (United States)

^c INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

^d JAPAN SCIENCE AND TECHNOLOGY AGENCY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BIOLOGY; COMPUTER; COMPUTER PROGRAM; MATHEMATICS; MOLECULAR MODEL; PRIORITY JOURNAL; SIMULATION; TECHNOLOGY;

EID: 0347511691     PISSN: 15362310     EISSN: None     Source Type: Journal    
DOI: 10.1089/153623103322637670     Document Type: Article

References (25)

1. BIOSPICE. (2001). The BioSPICE Development Project [On-line]. Available: www.biospice.org/.
2. BOX, D., EHNEBUSKE, D., KAKIVAYAT, G., et al. (2000). Simple object access protocol (SOAP) 1.1: W3C note 08 May 2000 [On-line]. Available: www.w3.org/TR/SOAP/.
3. BURNS, J.A. (1971). Studies on Complex Enzyme Systems [Ph.D. dissertation]. University of Edinburgh. Available: www.cds.caltech.edu/hsauro/Burns/jimBurns.pdf.
4. CHANCE, B., HIGGINS, J.J., and GARFINKEL, D. (1962). Analogue and digital computer representations of biochemical processes. Proc. Fed. Am. Soc. Exp Biol. 21, 75-86.
5. ELOWITZ, M.B., and LEIBLER, S. (2000). A synthetic oscillatory network of transcriptional regulators. Nature 403, 335-338.
6. ENDY, D., and BRENT, R. (2001). Modeling cellular behavior. Nature 409, 391-395.
7. FELL, D.A., and SAURO, H.M. (1990). Metabolic control analysis by computer: progress and prospects. Biomed. Biochim. Acta 8/9, 811-816.
8. GARFINKEL, D. (1968). A machine-independent language for the simulation of complex chemical and biochemical systems. Comput. Biomed. Res. 2, 31-44.
9. HEDLEY, W.J., MELANIE, N.R., BULLIVANT, D.P., et al. (2001). A short introduction to CellML. Phil. Trans. R. Soc. Lond. A 359, 1073-1089.
10. HUCKA, H.M., FINNEY, A., SAURO, H.M., et al. (2002). The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. Pac. Symp. Biocomput. 450-461.
11. HUCKA, M., FINNEY, A., SAURO, H.M., et al. (2003). The Systems Biology Markup Language (SBML): a medium for representation and exchange of biochemical network models. Bioinformatics 19, 524-531.
12. MENDES, P. (1993). Gepasi: a software package for modelling the dynamics, steady states and control of biochemical and other systems. Comput. Appl. Biosci. 9, 563-571.
13. OLSON, M., and OGBUJI, U. (2002). The Python web services developer: messaging technologies compared [On-line]. Available: www-106.ibm.com/developerworks/webservices/library/ws-pyth9/.
14. OMG. (2001). CORBA specication [On-line]. Available: www.omg.org.
15. ORAM, A. (2001). Peer-to-Peer: Harnessing the Power of Disruptive Technologies (O'Reilly & Associates, Sebastopol, CA).
16. PARK, D.J.M., and WRIGHT, B.E. (1973) Metasim, a general purpose metabolic simulator for studying cellular transformations. Comput. Prog. Biomed. 3, 10-26.
17. PFEIFFER, T., SANCHEZ-VALDENEBRO, I., NUNO, J.C., et al. (1999) Metatool: for studying metabolic networks. Bioinformatics 15, 251-257.
18. POOLMAN, M.G., FELL, D.A., and RAINES, C.A. (2003). Elementary modes analysis of photosynthate metabolism in the chloroplast stroma. Eur. J. Biochem. 270, 430-439.
19. PRITCHARD, L., and KELL, D.K. (2002). Schemes of flux control in a model of Saccharomyces cerevisiae glycolysis. Eur. J. Biochem. 269, 3894-3904.
20. RAO, D.M.W., and ARKIN, A.P. (2002). Control, exploitation and tolerance of intracellular noise. Nature 420, 231-237.
21. SAURO, H.M. (2000). Jarnac: a system for interactive metabolic analysis. In: Animating the Cellular Map: Proceedings of the 9th International Meeting on BioThermoKinetics. J.-H.S. Hofmeyr, J.M. Rohwer, and J.L. Snoep, eds. (Stellenbosch University Press), pp. 221-228.
22. SAURO, H.M., and FELL, D.A. (1991). Scamp: a metabolic simulator and control analysis program. Math. Comput. Modelling 15, 15-28.
23. SCHUSTER, S., FELL, D.A., and DANDEKAR, T. (2000). A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat. Biotechnol. 18, 326-332.
24. TYSON, J.J., CHEN, K.C., and NOVAK, B. (2003). Sniffers, buzzers, toggles and blinkers: dynamics of regulatory and signaling pathways in the cell. Curr. Opin. Cell Biol. 15, 221-231.
25. WINER, D. (2001). XML-RPC [On-line]. Available: www.xmlrpc.com/spec/.