Bio-PEPA: A framework for the modelling and analysis of biological systems
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[1] D. Gillespie,et al. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. , 2005, The Journal of chemical physics.
[2] Stephen Gilmore,et al. Modelling the Influence of RKIP on the ERK Signalling Pathway Using the Stochastic Process Algebra PEPA , 2006, Trans. Comp. Sys. Biology.
[3] Marta Z. Kwiatkowska,et al. Probabilistic model checking of complex biological pathways , 2008, Theor. Comput. Sci..
[4] Federica Ciocchetta. The BlenX Language with Biological Transactions , 2008, Trans. Comp. Sys. Biology.
[5] Corrado Priami,et al. Biological Transactions for Quantitative Models , 2007, Electron. Notes Theor. Comput. Sci..
[6] Luca Cardelli,et al. BioAmbients: an abstraction for biological compartments , 2004, Theor. Comput. Sci..
[7] Corrado Priami,et al. The BlenX Language: A Tutorial , 2008, SFM.
[8] Corrado Priami,et al. Beta-binders with Biological Transactions , 2006 .
[9] S. Gilmore,et al. Automatically deriving ODEs from process algebra models of signalling pathways , 2005 .
[10] Alberto Policriti,et al. Hybrid Systems and Biology , 2008, SFM.
[11] David R. Gilbert,et al. Analysis of Signalling Pathways Using Continuous Time Markov Chains , 2006, Trans. Comp. Sys. Biology.
[12] Corrado Priami,et al. Application of a stochastic name-passing calculus to representation and simulation of molecular processes , 2001, Inf. Process. Lett..
[13] Christel Baier,et al. Approximate Symbolic Model Checking of Continuous-Time Markov Chains , 1999, CONCUR.
[14] C. Rao,et al. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm , 2003 .
[15] A. Kierzek,et al. Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. , 2004, Biophysical journal.
[16] James W. Haefner,et al. Modeling Biological Systems , 1996, Springer US.
[17] Adam Duguid,et al. Stronger Computational Modelling of Signalling Pathways Using Both Continuous and Discrete-State Methods , 2006, CMSB.
[18] D. Herries. Enzyme Kinetics: Behaviour and Analysis of Rapid Equilibrium and Steady-State Enzyme Systems: By Irwin H. Segel. John Wiley & Sons, 1975. pp xxii + 957. Boards, £15.00 , 1976 .
[19] Nil Geisweiller,et al. Relating continuous and discrete PEPA models of signalling pathways , 2008, Theor. Comput. Sci..
[20] Jane Hillston,et al. Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks , 2007, FBTC@CONCUR.
[21] J. Rawlings,et al. Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics , 2002 .
[22] Corrado Priami,et al. The Beta Workbench , 2007 .
[23] Paola Lecca,et al. A Stochastic Process Algebra Approach to Simulation of Autoreactive Lymphocyte Recruitment , 2004, Simul..
[24] M Hucka,et al. Evolving a lingua franca and associated software infrastructure for computational systems biology: the Systems Biology Markup Language (SBML) project. , 2004, Systems biology.
[25] Alberto Policriti,et al. Modeling Biological Systems in Stochastic Concurrent Constraint Programming , 2008, Constraints.
[26] D. Gillespie. Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .
[27] Maria Luisa Guerriero,et al. Modelling Biological Compartments in Bio-PEPA , 2008, MeCBIC.
[28] Corrado Priami,et al. Modeling Kohn Interaction Maps with Beta-Binders: An Example , 2005, Trans. Comp. Sys. Biology.
[29] Vincent Danos,et al. Formal Molecular Biology Done in CCS-R , 2007, Electron. Notes Theor. Comput. Sci..
[30] Cosimo Laneve,et al. A Simple Calculus for Proteins and Cells , 2007, Electron. Notes Theor. Comput. Sci..
[31] Kwang-Hyun Cho,et al. Modeling and simulation of intracellular dynamics: choosing an appropriate framework , 2004, IEEE Transactions on NanoBioscience.
[32] Robert K. Brayton,et al. Verifying Continuous Time Markov Chains , 1996, CAV.
[33] Vincent Danos,et al. Formal Molecular Biology done in CCS , 2003 .
[34] Alberto Policriti,et al. Stochastic Concurrent Constraint Programming and Differential Equations , 2007, QAPL.
[35] J J Collins,et al. A theory for controlling cell cycle dynamics using a reversibly binding inhibitor. , 1998, Proceedings of the National Academy of Sciences of the United States of America.
[36] Jacky L. Snoep,et al. BioModels Database: a free, centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems , 2005, Nucleic Acids Res..
[37] R. Bundschuh,et al. Fluctuations and slow variables in genetic networks. , 2003, Biophysical Journal.
[38] Hamid Bolouri,et al. Dizzy: Stochastic Simulation of Large-scale Genetic Regulatory Networks , 2005, J. Bioinform. Comput. Biol..
[39] Vincent Danos,et al. Scalable Simulation of Cellular Signaling Networks , 2007, APLAS.
[40] Vincent Danos,et al. Abstract Interpretation of Cellular Signalling Networks , 2008, VMCAI.
[41] Jane Hillston,et al. A compositional approach to performance modelling , 1996 .
[42] Corrado Priami,et al. Modelling and simulation of biological processes in BlenX , 2008, PERV.
[43] Joachim Niehren,et al. Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch , 2006, Trans. Comp. Sys. Biology.
[44] Vincent Danos,et al. Rule-Based Modelling of Cellular Signalling , 2007, CONCUR.
[45] François Fages,et al. Modelling and querying interaction networks in the biochemical abstract machine BIOCHAM , 2002 .
[46] A Goldbeter,et al. A minimal cascade model for the mitotic oscillator involving cyclin and cdc2 kinase. , 1991, Proceedings of the National Academy of Sciences of the United States of America.
[47] E. Gilles,et al. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors , 2002, Nature Biotechnology.
[48] Corrado Priami,et al. Beta Binders for Biological Interactions , 2004, CMSB.
[49] M. Kanehisa. A database for post-genome analysis. , 1997, Trends in genetics : TIG.
[50] M. Elowitz,et al. A synthetic oscillatory network of transcriptional regulators , 2000, Nature.
[51] Stephen Gilmore,et al. Integrated Simulation and Model-Checking for the Analysis of Biochemical Systems , 2009, Electron. Notes Theor. Comput. Sci..
[52] Cosimo Laneve,et al. Formal molecular biology , 2004, Theor. Comput. Sci..
[53] Muffy Calder,et al. Some Investigations Concerning the CTMC and the ODE Model Derived From Bio-PEPA , 2009, FBTC@ICALP.