Русская версия English version   
О журнале
Редакционная коллегия
Правила для авторов
Информация для читателей и авторов
Оглавление текущего номера
Архив
Контакты
Поиск

Отправить статью
 


Том 2   Выпуск 2   Год 2007
Лахно В., Назипова Н., Ким В., Филиппов С., Фиалко Н., Устинин Д., Теплухин А., Тюльбашева Г., Зайцев А., Устинин М.

Информационно-вычислительная среда Mathcell для моделирования живой клетки

Математическая биология и биоинформатика. 2007;2(2):361-376.

doi: 10.17537/2007.2.361.

Список литературы

  1. Grinchenko SN, Zaguskin SL. Mekhanizmy zhivoi kletki: algoritmicheskaia model' (Mechanisms of a Living Cell: An Algorithmic Model). Moscow; 1989. 232 p. (in Russ.).
  2. Normile D. Building Working Cells ‘In Silico’. Science. 1999;284:80-81. doi: 10.1126/science.284.5411.80b
  3. Triendl R. Computerized role models. Nature. 2002;417:7.
  4. E-CELL Project Home Page. http://www.e-cell.org/ecell/ (accessed 01 November 2007).
  5. Tomita M, Hashimoto K, Takahashi K, Shimizu TS, Matsuzaki Y, Miyoshi F, Saito K, Tanida S, Yugi K, Venter JC, Hutchison CA 3rd. E-CELL: software environment for whole-cell simulation. Bioinformatics. 1999;15(1);72-84. doi: 10.1093/bioinformatics/15.1.72
  6. National Resource for Cell Analysis and Modeling. http://vcell.org/ (accessed 01 July 2013).
  7. BioUML - open source Java framework for systems biology. http://www.biouml.org/ (accessed 01 July 2013).
  8. Center for Cell and Virus Theory. Cell Modelling Page. http://biodynamics.indiana.edu/CellModeling (accessed 01 November 2007).
  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 LC. The Karyote physico-chemical genomic, proteomic, metabolic cell modeling system. OMICS. 2003;7(3):269-283. doi: 10.1089/153623103322452396
  10. BioNetGen – Biological Network Generator. http://cellsignaling.lanl.gov/bionetgen (accessed 01 July 2013).
  11. Faeder JR, Blinov ML, Goldstein B, Hlavacek WS. Rule-based modeling of biochemical networks. Complexity. 2005;10:22-41. doi: 10.1002/cplx.20074
  12. Blinov ML, Faeder JR, Goldstein B, Hlavacek WS. BioNetGen: software for rule-based modeling of signal transduction based on the interactions of molecular domains. Bioinformatics. 2004;20(17):3289-3291. doi: 10.1093/bioinformatics/bth378
  13. Sauro HM, Hucka M, Finney A, Wellock C, Bolouri H, Doyle J, Kitano H. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. OMICS. 2003;7(4):355-372. doi: 10.1089/153623103322637670
  14. Dhar PK, Meng TCh, Somani S, Li Ye, Sakharkar K, Krishnan A, Ridwan ABM, Ho Kok Wah S, Chitre M, Zhu Hao. Grid Cellware: the first grid-enabled tool for modelling and simulating cellular processes. Bioinformatics. 2005;21(7). doi: 10.1093/bioinformatics/bti143
  15. Cellware: A New Modeling and Simulation Tool for Modeling Cellular Transactions. http://www.bii.a-star.edu.sg/research/sbg/cellware/ (accessed 01 November 2007).
  16. Systems Biology Markup Language. http://sbml.org/index.psp (accessed 01 July 2013).
  17. Extensible Markup Language (XML) 1.0. Fourth Edition. http://www.w3.org/TR/REC-xml/ (accessed 01 July 2013).
  18. World Wide Web Consortium. http://www.w3.org/ (accessed 01 July 2013).
  19. Finney A, Hucka M. Systems Biology Markup Language: Level 2 and Beyond. Biochem. Soc. Trans. 2003;31:1472-1473.
  20. Finney A. Developing SBML Beyond Level 2: Proposals for Development. Lecture Notes in Computer Science. 2005;3082:242-247. doi: 10.1007/978-3-540-25974-9_21
  21. Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H, Arkin AP, Bornstein BJ, Bray D, Cornish-Bowden A, Cuellar AA, Dronov S, Gilles ED, Ginkel M, Gor V, Goryanin II, Hedley WJ, Hodgman TC, Hofmeyr JH, Hunter PJ, Juty NS, Kasberger JL, Kremling A, Kummer U, Le Novère N, Loew LM, Lucio D, Mendes P, Minch E, Mjolsness ED, Nakayama Y, Nelson MR, Nielsen PF, Sakurada T, Schaff JC, Shapiro BE, Shimizu TS, Spence HD, 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. 2003;19(4):524-531. doi: 10.1093/bioinformatics/btg015
  22. Shapiro BE, Hucka M, Finney A, Doyle J. MathSBML: a package for manipulating SBML-based biological models. Bioinformatics. 2004;20(16):2829-2831. doi: 10.1093/bioinformatics/bth271
  23. CellML Home Page. http://www.cellml.org/ (accessed 01 July 2013).
  24. Cuellar AA, Lloyd CM, Nielsen PF, Bullivant DP, Nickerson DP, Hunter PJ. An Overview of CellML 1.1, a Biological Model Description Language. SIMULATION: Transactions of The Society for Modeling and Simulation International. 2003;79(12):740-747. doi: 10.1177/0037549703040939
  25. Lloyd CM, Halstead MDB, Nielsen PF. CellML: its future, present and past. Progress in Biophysics and Molecular Biology. 2004;85(2-3):433-450. doi: 10.1016/j.pbiomolbio.2004.01.004
  26. Schilstra MJ, Li L, Matthews J, Finney A, Hucka M, Le Novère N. CellML2SBML: conversion of CellML into SBML. Bioinformatics. 2006;22(8):1018-1020. doi: 10.1093/bioinformatics/btl047
  27. The BioModels Database. http://www.ebi.ac.uk/biomodels/ (accessed 01 July 2013).
  28. Le Novere N, Bornstein B, Broicher A, Courtot M, Donizelli M, Dharuri H, Li L, Sauro H, Schilstra M, Shapiro B, Snoep JL, Hucka M. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Res. 2006;34:D689-D691. doi: 10.1093/nar/gkj092
  29. BioPAX: Biological Pathways Exchange. http://www.biopax.org/ (accessed 01 July 2013).
  30. Fisher IZ. Statistical Theory of Liquids. University of Chicago Press; 1964.
  31. Poltev VI, Grokhlina TI, Malenkov GG. J. Biomol. Struct. Dyn. 1984;2:413-429.
  32. Poltev VI, Malenkov GG, Gonzalez EJ, Teplukhin AV, Rein R, Shibata M, Miller JH. J. Biomol. Struct. Dyn. 1996;13:717-725.
Содержание
Оригинальная статья
Мат. биол. и биоинф.
2007;2(2):361-376
doi: 10.17537/2007.2.361
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы

 
  Copyright ИМПБ РАН © 2005-2024