Modular modeling of cellular systems with ProMoT/Diva

Bioinformatics

Volumn 19, Issue 9, 2003, Pages 1169-1176

  Ginkel, M ^a   Kremling, A ^a   Nutsch, T ^a   Rehner, R ^a   Gilles, E D ^a  

^a MPI for Dynamics of Complex Technical Systems   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; ARTICLE; BIOLOGICAL MODEL; CELL; CELL FUNCTION; COMPUTER INTERFACE; COMPUTER PROGRAM; COMPUTER SIMULATION; COMPUTER SYSTEM; CYTOLOGY; FACTUAL DATABASE; MATHEMATICAL COMPUTING; MATHEMATICAL MODEL; METABOLISM; METHODOLOGY; PARAMETRIC TEST; PHYSIOLOGY; PRIORITY JOURNAL; SIMULATION;

EID: 0037715313     PISSN: 13674803     EISSN: 13674811     Source Type: Journal    
DOI: 10.1093/bioinformatics/btg128     Document Type: Article

References (23)

1. Baltes,M., Schneider,R., Sturm,C. and Reuss,M. (1994) Optimal experimental design for parameter estimation in unstructured growth models. Biotechn. Progr., 10, 480-488.
2. Gilles,E.D. (1998) Network theory for chemical processes. Chemical Engineering and Technology, 21, 121-132.
3. Goryanin,I., Hodgman,T. and Selkov,E. (1999) Mathematical simulation and analysis of cellular metabolism and regulation. Bioinformatics, 15, 749-758.
4. Heinrich,R. and Schuster,S. (1996) The Regulation of Cellular Processes. Chapman and Hall, London.
5. Hucka,M., Finney,A., Sauro,H.M., Bolouri,H., Doyle,J.C., Kitano,H. and the rest of the SBML forum, (2003) The systems biology markup language (sbml): a medium for representation and exchange of biochemical network models. Bioinformatics, 19, 524-531.
6. Kanehisa,M. and Goto,S. (2000) KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res., 28, 27-30.
7. Kiczales,G., des Rivières,J. and Bobrow,.D.G. (1991) The Art of the Metaobject Protocol. MIT Press, Cambridge, MA.
8. Köhler,R., Räumschüssel,S. and Zeitz,M. (1997) Code generator for implementing differential algebraic models used in the process simulation tool DIVA. In Proceedings of 15th IMACS World Congress. Berlin, pp. 621-626.
9. Kremling,A. and Gilles,E.D. (2001) The organization of metabolic reaction networks: II. Signal processing in hierarchical structured functional units. Metab. Eng., 3, 138-150.
10. Kremling,A., Jahreis,K., Lengeler,J.W. and Gilles,E.D. (2000) The organization of metabolic reaction networks: a signal-oriented approach to cellular models. Metab. Eng., 2, 190-200.
11. Kremling,A., Bettenbrock,K., Laube,B., Jahreis,K., Lengeler,J.W. and Gilles,E.D. (2001) The organization of metabolic reaction networks: III. Application for diauxic growth on glucose and lactose. Metab. Eng., 3, 362-379.
12. Ljung,L. (1999) System Identification-Theory for the User, Second edn, Prentice Hall PTR, Upper Saddle River, NJ.
13. Mendes,P. (September 1997) Biochemistry by numbers: simulation of biochemical pathways with GEPASI 3. Trends Biochem. Sci., 22, 361-363.
14. Mohl,K.D., Spieker,A., Köhler,R., Gilles,E.D. and Zeitz,M. (1997) DIVA-A simulation environment for chemical engineering applications. ICCS Collect. Vol. Sci. Pap. Donetsk State Techn. University, Ukraine, pp. 8-15.
15. Moré,J.J. and Wright,S.J. (1993) Optimization Software Guide. SIAM, Philadelphia, PA.
16. Neidhardt,F.C., Ingraham,J.L. and Schaechter,M. (1990) Physiology of the Bacterial Cell: a Molecular Approach. Sinauer, Sunderland, MA.
17. Posten,C. and Munack,A. (1990) On-line application of parameter estimation accuracy to biotechnical processes. In Proceedings of ACC. 3, pp. 2181-2186.
18. Salgado,H., Santos,A., Gama-Castro,S., Millan-Zarate,D., Diaz-Peredo,E., Sanchez-Solano,F., Perez-Rueda,E., Bonavides-Martinez,C. and Collado-Vides,J. (2001) RegulonDB (version 3.2): transcriptional regulation and operon organization in Escherichia coli k-12. Nucleic Acids Res., 72-74.
19. 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, South Africa, pp. 221-228.
20. Schaefer,U., Boos,W., Takors,R. and Weuster-Botz,D. (1999) Automated sampling device for monitoring mracellular metabolite ynamics. Analyt. Biochem., 270, 88-96.
21. Schaff,J., Fink,C.C., Slepchenko,B., Carson,J.H. and Loew,L.M. (1997) A general computational framework for modeling cellular structure and function. Biophys. J..
22. Tomita,M., Hashimoto,K., Takahashi,K., Shimizu,T.S., Matsuzaki,Y., Miyoshi,F., Saito,K., Tanida,S., Yugi,K., Venter,J.G. and Hutchison III,C.A. (1999) E-CELL: software environment for whole-cell simulation. Bioinformatis, 15, 72-84.
23. Tränkle,F., M.,Zeitz, Ginkel,M. and Gilles,E.D. (2000) Promot: a modeling tool for chemical processes. MCMDS, 6, 283-307.