COPASI - a COmplex PAthway SImulator
暂无分享,去创建一个
Mudita Singhal | Liang Xu | Natalia Simus | Sven Sahle | Ursula Kummer | Pedro Mendes | Stefan Hoops | Ralph Gauges | Christine Lee | Jürgen Pahle | P. Mendes | J. Pahle | R. Gauges | S. Sahle | S. Hoops | U. Kummer | M. Singhal | Christine Lee | N. Simus | Liang Xu
[1] D. Fell. Understanding the Control of Metabolism , 1996 .
[2] Masaru Tomita,et al. E-CELL: software environment for whole-cell simulation , 1999, Bioinform..
[3] Catherine M Lloyd,et al. CellML: its future, present and past. , 2004, Progress in biophysics and molecular biology.
[4] Melvin K. Simmons,et al. Hybrid simulation of cellular behavior , 2004, Bioinform..
[5] Kenneth Levenberg. A METHOD FOR THE SOLUTION OF CERTAIN NON – LINEAR PROBLEMS IN LEAST SQUARES , 1944 .
[6] J. Stucki,et al. Stability analysis of biochemical systems--a practical guide. , 1978, Progress in biophysics and molecular biology.
[7] Takuji Nishimura,et al. Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator , 1998, TOMC.
[8] Xin Yao,et al. Stochastic ranking for constrained evolutionary optimization , 2000, IEEE Trans. Evol. Comput..
[9] Douglas B. Kell,et al. Non-linear optimization of biochemical pathways: applications to metabolic engineering and parameter estimation , 1998, Bioinform..
[10] C. Rao,et al. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .
[11] D. Gillespie. A General Method for Numerically Simulating the Stochastic Time Evolution of Coupled Chemical Reactions , 1976 .
[12] Hong Li,et al. Efficient formulation of the stochastic simulation algorithm for chemically reacting systems. , 2004, The Journal of chemical physics.
[13] Pedro Mendes,et al. GEPASI: a software package for modelling the dynamics, steady states and control of biochemical and other systems , 1993, Comput. Appl. Biosci..
[14] Steffen Klamt,et al. FluxAnalyzer: exploring structure, pathways, and flux distributions in metabolic networks on interactive flux maps , 2003, Bioinform..
[15] Hiroaki Kitano,et al. The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..
[16] A. Wolf,et al. Determining Lyapunov exponents from a time series , 1985 .
[17] E Bornberg-Bauer,et al. Switching from simple to complex oscillations in calcium signaling. , 2000, Biophysical journal.
[18] D. Marquardt. An Algorithm for Least-Squares Estimation of Nonlinear Parameters , 1963 .
[19] Ed Anderson,et al. LAPACK Users' Guide , 1995 .
[20] Robert Hooke,et al. `` Direct Search'' Solution of Numerical and Statistical Problems , 1961, JACM.
[21] Hiroaki Kitano,et al. Next generation simulation tools: the Systems Biology Workbench and BioSPICE integration. , 2003, Omics : a journal of integrative biology.
[22] L. Petzold. Automatic Selection of Methods for Solving Stiff and Nonstiff Systems of Ordinary Differential Equations , 1983 .
[23] P Mendes,et al. Biochemistry by numbers: simulation of biochemical pathways with Gepasi 3. , 1997, Trends in biochemical sciences.
[24] Yang Cao,et al. Multiscale stochastic simulation algorithm with stochastic partial equilibrium assumption for chemically reacting systems , 2005 .
[25] R. Heinrich,et al. The Regulation of Cellular Systems , 1996, Springer US.
[26] James Demmel,et al. LAPACK Users' Guide, Third Edition , 1999, Software, Environments and Tools.
[27] A. Kierzek,et al. Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. , 2004, Biophysical journal.
[28] Herbert M. Sauro,et al. Conservation analysis of large biochemical networks , 2006, Bioinform..
[29] Hao Zhu,et al. Cellware-a multi-algorithmic software for computational systems biology , 2004, Bioinform..
[30] Michael A. Gibson,et al. Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels , 2000 .
[31] S. Goldfeld,et al. Maximization by Quadratic Hill-Climbing , 1966 .
[32] D. Fell,et al. Detection of elementary flux modes in biochemical networks: a promising tool for pathway analysis and metabolic engineering. , 1999, Trends in biotechnology.
[33] Juan Carlos Nuño,et al. METATOOL: for studying metabolic networks , 1999, Bioinform..
[34] Wilhelm Huisinga,et al. ADAPTIVE SIMULATION OF HYBRID STOCHASTIC AND DETERMINISTIC MODELS FOR BIOCHEMICAL SYSTEMS , 2005 .
[35] Ursula Kummer,et al. Transition from stochastic to deterministic behavior in calcium oscillations. , 2005, Biophysical journal.
[36] Yiannis Kaznessis,et al. Accurate hybrid stochastic simulation of a system of coupled chemical or biochemical reactions. , 2005, The Journal of chemical physics.
[37] Zbigniew Michalewicz,et al. Genetic Algorithms + Data Structures = Evolution Programs , 1992, Artificial Intelligence.
[38] J. Rawlings,et al. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics , 2002 .
[39] Charles L. Lawson,et al. Basic Linear Algebra Subprograms for Fortran Usage , 1979, TOMS.
[40] J. Hofmeyr,et al. Metabolic regulation: A control analytic perspective , 1995, Journal of bioenergetics and biomembranes.
[41] David B. Fogel,et al. Meta-evolutionary programming , 1991, [1991] Conference Record of the Twenty-Fifth Asilomar Conference on Signals, Systems & Computers.
[42] Vassilios Sotiropoulos,et al. Multiscale Hy3S: Hybrid stochastic simulation for supercomputers , 2006, BMC Bioinformatics.
[43] Nicolas Le Novère,et al. STOCHSIM: modelling of stochastic biomolecular processes , 2001, Bioinform..