Integrated mathematical model of the living cell
Matematičeskaâ biologiâ i bioinformatika, Tome 2 (2007) no. 2, pp. 361-376.

Voir la notice de l'article provenant de la source Math-Net.Ru

The informational and computational web-portal “Mathematical Cell” (http://www.mathcell.ru), which has been created by the collective body, is described. "Mathematical Cell' includes a 3D-model of the eukaryotic cell, an encyclopedia of knowledge in mathematical biology, and a collection of original models of individual cell processes. The 3D-model is furnished with browsing facilities in the internal space and connected with the informational component of the portal.
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V. D. Lakhno; N. N. Nazipova; V. L. Kim; S. V. Filippov; N. S. Fialko; D. M. Ustinin; A. V. Teplukhin; G. È. Tyulbasheva; A. Yu. Zaitsev; M. N. Ustinin. Integrated mathematical model of the living cell. Matematičeskaâ biologiâ i bioinformatika, Tome 2 (2007) no. 2, pp. 361-376. http://geodesic.mathdoc.fr/item/MBB_2007_2_2_a3/

[1] S. Grinchenko, S. Zaguskin, Mekhanizmy zhivoi kletki: algoritmicheskaya model, Nauka, M., 1989, 232 pp. | Zbl

[2] D. Normile, “Building Working Cells 'In Silico'”, Science, 284 (1999), 80–81

[3] R. Triendl, “Computerized role models”, Nature, 417 (2002), 7

[4] E-CELL Project Home Page, http://www.e-cell.org/ecell/

[5] Tomita M., Hashimoto K., Takahashi K., Shimizu T. S., Matsuzaki Y., Miyoshi F., Saito K., Tanida S., Yugi K., Venter J. C., Hutchison C. A., “E-CELL: software environment for whole-cell simulation”, Bioinformatics, 15:1 (1999), 72–84 | DOI

[6] National Resource for Cell Analysis and Modeling, http://vcell.org/

[7] BioUML – open source Java framework for systems biology, http://www.biouml.org/

[8] Center for Cell and Virus Theory. Cell Modelling Page, http://biodynamics.indiana.edu/ CellModeling

[9] Ortoleva P., Berry E., Brun Y., Fan J., Fontus M., Hubbard K., Jaqaman K., Jarymowycz L., Navid A., Sayyed-Ahmad A., Shreif Z., Stanley F., Tuncay K., Weitzke E., Wu L. C., “The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system”, OMICS, 7:3 (2003), 269–283 | DOI

[10] BioNetGen – Biological Network Generator, http://cellsignaling.lanl.gov/ bionetgen

[11] J. R. Faeder, M. L. Blinov, B. Goldstein and W. S. Hlavacek, “Rule-based modeling of biochemical networks”, Complexity, 10 ((2005), 22–41 | DOI

[12] Blinov M. L., Faeder J. R., Goldstein B., Hlavacek W S., “BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains”, Bioinformatics, 20:17 (2004), 3289–3291 | DOI

[13] Sauro H. M., Hucka M., Finney A., Wellock C., Bolouri H., Doyle J. and Kitano H., “Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration”, OMICS, 7:4 (2003), 355–372 | DOI

[14] P. K. Dhar, T. Ch. Meng, S. Somani, Li Ye, K. Sakharkar, A. Krishnan, A. B. M. Ridwan, S. Ho Kok Wah, M. Chitre, Zhu Hao, “Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes”, Bioinformatics, 21:7 (2005), 1284–1287 | DOI | MR

[15] Cellware: A New Modeling and Simulation Tool for Modeling Cellular Transactions, http://www.bii.a-star.edu.sg/research/sbg/cellware/

[16] Systems Biology Markup Language, http://sbml.org/index.psp

[17] Extensible Markup Language (XML) 1.0 (Fourth Edition), http://www.w3.org/TR/RECxml/

[18] World Wide Web Consortium, http://www.w3.org/

[19] A. Finney and M. Hucka, “Systems Biology Markup Language: Level 2 and Beyond”, Biochem. Soc. Trans., 31 (2003), 1472–1473 | DOI

[20] A. Finney, “Developing SBML Beyond Level 2: Proposals for Development”, Lecture Notes in Computer Science, 3082, 2005, 242–247 | Zbl

[21] Hucka M., Finney A., Sauro H. M., Bolouri H., Doyle J. C., Kitano H., Arkin A. P., Bornstein B. J., Bray D., Cornish-Bowden A., Cuellar A. A., Dronov S., Gilles E. D., Ginkel M., Gor V., Goryanin II, Hedley W. J., Hodgman T. C., Hofmeyr J. H., Hunter P. J., Juty N. S., Kasberger J. L., Kremling A., Kummer U., Le Novere N., Loew L. M., Lucio D., Mendes P., Minch E., Mjolsness E. D., Nakayama Y., Nelson M. R., Nielsen P. F., Sakurada T., Schaff J. C., Shapiro B. E., Shimizu T. S., Spence H. D., Stelling J., Takahashi K., Tomita M., Wagner J., Wang J., “SBML Forum. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models”, Bioinformatics, 19:4 (2003), 524–531 | DOI

[22] Shapiro B. E., Hucka M., Finney A., Doyle J., “MathSBML: a package for manipulating SBML-based biological models”, Bioinformatics, 20:16 (2004), 2829–2831 | DOI

[23] CellML Home Page, http://www.cellml.org/

[24] Cuellar A. A., Lloyd C. M., Nielsen P. F., Bullivant D. P., Nickerson D. P. and Hunter P. J., “An Overview of CellML 1.1, a Biological Model Description Language”, SIMULATION: Transactions of The Society for Modeling and Simulation International, 79:12 (2003), 740–747 | DOI

[25] Lloyd C. M., Halstead M. D. B. and Nielsen P. F., “CellML: its future, present and past”, Progress in Biophysics and Molecular Biology, 85:2–3 (2004), 433–450 | DOI

[26] Schilstra M. J., Li L., Matthews J., Finney A., Hucka M., Le Novere N., “CellML2SBML: conversion of CellML into SBML”, Bioinformatics, 22:8 (2006), 1018–1020 | DOI

[27] The BioModels Database, http://www.ebi.ac.uk/biomodels/

[28] Le Novere N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J. L., Hucka M., “BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems”, Nucleic Acids Res., 34 (2006), D689–D691 | DOI

[29] BioPAX : Biological Pathways Exchange, http://www.biopax.org/

[30] Fisher I. Z., Statisticheskaya teoriya zhidkostei, GIFML, M., 1961, 280 pp.

[31] Poltev V. I., Grokhlina T. I. and Malenkov G. G., J. Biomol. Struct. Dyn., 2 (1984), 413–429

[32] Poltev V. I., Malenkov G. G., Gonzalez E. J., Teplukhin A. V., Rein R., Shibata M. and Miller J. H., J. Biomol. Struct. Dyn., 13 (1996), 717–725