References
- D.-Y. Lee, C. Yun, B. K. Hou, S. Park and S. Y. Lee, 'WebCell: a web-based environment for kinetic modeling and dynamic simulation of cellula networks,' submitted
- S. Y. Lee, D.-Y. Lee and T. Y. Kim, 'Systems biotechnology for strain improvement,' Trends in Biotechnology, vol. 23, pp. 349-358, 2005 https://doi.org/10.1016/j.tibtech.2005.05.003
- I. Goryanin, T. C. Hodgman and E. Selkov, 'Mathematical simulation and analysis of cellular metabolism and regulation,' Bioinformatics, vol. 15, pp. 749-758, 1999 https://doi.org/10.1093/bioinformatics/15.9.749
- U. M. Ascher and L. R. Petzold, 'Computer methods for ordinary differential equations and differential-algebraic equations,' SIAM, 1998
- T. C. Meng, S. Somani and P. Dhar, 'Modelling and simulation of biological systems with stochasticity,' In Silico Biology, vol. 4,0024,2004
- N. Novere and T. S. Shimizu, 'Stochsim: Modeling of Stochastic Biomolecular Processes,' Bioinformatics, vol. 6, pp. 575-576, 2001 https://doi.org/10.1093/bioinformatics/17.6.575
- T. R. Kiehl, R. M. Mattheyses and M. K. Simmons, 'Hybrid simulation of cellular behavior,' Bioinformatics, vol. 20, pp. 316-322, 2004 https://doi.org/10.1093/bioinformatics/btg409
- D.-Y. Lee, H. Yun, S. Park and S. Y. Lee, 'MetaFluxNet: the management of metabolic reaction information and quantitative metabolic flux analysis,' Bioinformatics, vol. 19, pp. 2144-2146, 2003 https://doi.org/10.1093/bioinformatics/btg271
- M. Tomita, K. Hashimoto, K. Takahashi, T. S. Shimizu, Y. Matsuzaki, F. Miyoshi et al., 'E-CELL: software environment for whole-cell simulation,' Bioinformatics, vol. 15, pp. 72-84, 1999 https://doi.org/10.1093/bioinformatics/15.1.72
- P. Mendes, 'Biochemistry by numbers: simulation of biochemical pathways with Gepasi3,' Trends Biochem. Sci., vol. 22, pp. 361-363, 1997 https://doi.org/10.1016/S0968-0004(97)01103-1
- L. M. Loew and J. C. Schaff, 'The Virtual Cell: A Software Environment for Computational Cell Biology,' Trends Biotechnol., vol. 19, pp. 401-406, 2001 https://doi.org/10.1016/S0167-7799(01)01740-1
- B. G. Olivier and J. L. Snoep, 'Web-based kinetic modeling using JWS Online,' Bioinformatics, vol. 20, pp. 2143-2144, 2004 https://doi.org/10.1093/bioinformatics/bth200
- M. Hucka, A. Finney, H. M. Sauro, H. Bolouri, J. C. Doyle and H. Kitano, 'The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models,' Bioinformatics, vol. 19, pp. 524-531, 2002 https://doi.org/10.1093/bioinformatics/btg015
- M. Hucka, A. Finney, B. J. Bornstein et al., 'Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project,' Systems Biology, vol. 1, pp. 41-53, 2004 https://doi.org/10.1049/sb:20045008
- B. G. Oliver, J. M. Rohwer and J. S. Hofmeyr 'Modeling cellular systems with PySCeS,' Bioinformatics, vol. 21, pp. 560-561, 2005 https://doi.org/10.1093/bioinformatics/bti046
- S. Kimura, T. Kawasaki, M. Hatakeyarma, T. Naka, F. Konishi and A. Konagaya, 'OBIYagns: a grid-based biochemical simulator with a parameter estimator,' Bioinformatics, vol. 20, pp. 1646-1648, 2004 https://doi.org/10.1093/bioinformatics/bth122
- H. M. Sauro, B. Ingalls, 'Conservation analysis in biochemical networks: computational issues for software writers,' Biophys. Chem. J., vol. 109, pp. 1-15, 2004 https://doi.org/10.1016/j.bpc.2003.08.009
- D. A. Beard S. D. Liang and H. Qian, 'Energy balance for analysis of complex metabolic networks,' Biophys. J., vol. 83, pp. 79-86, 2002 https://doi.org/10.1016/S0006-3495(02)75150-3
- S. Okino and M. L. Mavrovouniotis, 'Simplification of mathematical models of chemical reaction systems,' Chemical Reviews, vol. 98, 1998
- M. Schauer, R. Heinrich, 'Quasi-steady-state approximation in the mathematical modeling of biochemical reaction networks,' Mathematical Biosciences, vol. 65, pp. 155-170, 1983 https://doi.org/10.1016/0025-5564(83)90058-5