Formalisms for Specifying Markovian Population Models

We compare several languages for specifying Markovian population models such as queuing networks and chemical reaction networks. These languages --matrix descriptions, stochastic Petri nets, stoichiometric equations, stochastic process algebras, and guarded command models-- all describe continuous-time Markov chains, but they differ according to important properties, such as compositionality, expressiveness and succinctness, executability, ease of use, and the support they provide for checking the well-formedness of a model and for analyzing a model.

[1]  Corrado Priami,et al.  Stochastic pi-Calculus , 1995, Comput. J..

[2]  L. You,et al.  Stochastic vs. deterministic modeling of intracellular viral kinetics. , 2002, Journal of theoretical biology.

[3]  A. Arkin,et al.  It's a noisy business! Genetic regulation at the nanomolar scale. , 1999, Trends in genetics : TIG.

[4]  P. Swain,et al.  Intrinsic and extrinsic contributions to stochasticity in gene expression , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[5]  Souheib Baarir,et al.  The GreatSPN tool: recent enhancements , 2009, PERV.

[6]  J. Hillston The nature of synchronisation , 1994 .

[7]  J. Paulsson Summing up the noise in gene networks , 2004, Nature.

[8]  Micha Yadin,et al.  Randomization Procedures in the Computation of Cumulative-Time Distributions over Discrete State Markov Processes , 1984, Oper. Res..

[9]  Marta Z. Kwiatkowska,et al.  PRISM: probabilistic model checking for performance and reliability analysis , 2009, PERV.

[10]  A. Jensen,et al.  Markoff chains as an aid in the study of Markoff processes , 1953 .

[11]  T. Henzinger,et al.  Executable cell biology , 2007, Nature Biotechnology.

[12]  C. Rao,et al.  Control, exploitation and tolerance of intracellular noise , 2002, Nature.

[13]  Hiroaki Kitano,et al.  The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models , 2003, Bioinform..

[14]  W. J. Anderson Continuous-Time Markov Chains: An Applications-Oriented Approach , 1991 .

[15]  Thomas A. Henzinger,et al.  Approximation of event probabilities in noisy cellular processes , 2009, Theor. Comput. Sci..

[16]  Darren J. Wilkinson Stochastic Modelling for Systems Biology , 2006 .

[17]  William H. Sanders,et al.  Reduced base model construction methods for stochastic activity networks , 1989, Proceedings of the Third International Workshop on Petri Nets and Performance Models, PNPM89.

[18]  P. Buchholz Exact and ordinary lumpability in finite Markov chains , 1994, Journal of Applied Probability.

[19]  Joost-Pieter Katoen,et al.  A Markov reward model checker , 2005, Second International Conference on the Quantitative Evaluation of Systems (QEST'05).

[20]  Peter J. Haas,et al.  Stochastic Petri Nets , 2002 .

[21]  J. Collins,et al.  Construction of a genetic toggle switch in Escherichia coli , 2000, Nature.

[22]  Thomas A. Henzinger,et al.  Reactive Modules , 1999, Formal Methods Syst. Des..

[23]  PETER BUCHHOLZ,et al.  Block SOR Preconditioned Projection Methods for Kronecker Structured Markovian Representations , 2005, SIAM J. Sci. Comput..

[24]  Jan J. M. M. Rutten,et al.  Mathematical techniques for analyzing concurrent and probabilistic systems , 2004, CRM monograph series.

[25]  William J. Stewart,et al.  Introduction to the numerical solution of Markov Chains , 1994 .

[26]  K. Burrage,et al.  Stochastic models for regulatory networks of the genetic toggle switch. , 2006, Proceedings of the National Academy of Sciences of the United States of America.

[27]  William H. Sanders,et al.  "On-the-Fly'' Solution Techniques for Stochastic Petri Nets and Extensions , 1998, IEEE Trans. Software Eng..

[28]  Jane Hillston,et al.  A compositional approach to performance modelling , 1996 .

[29]  W. Stewart,et al.  The numerical solution of stochastic automata networks , 1995 .

[30]  Nieves R. Brisaboa,et al.  Approximate computation of transient results for large Markov chains , 2004 .

[31]  W. J. Anderson Continuous-Time Markov Chains , 1991 .

[32]  Paulo Fernandes,et al.  Numerical evaluation of stochastic automata networks , 1995, MASCOTS '95. Proceedings of the Third International Workshop on Modeling, Analysis, and Simulation of Computer and Telecommunication Systems.

[33]  Thomas A. Henzinger,et al.  Sliding Window Abstraction for Infinite Markov Chains , 2009, CAV.

[34]  Donald Gross,et al.  The Randomization Technique as a Modeling Tool and Solution Procedure for Transient Markov Processes , 1984, Oper. Res..

[35]  Edsger W. Dijkstra,et al.  Guarded commands, nondeterminacy and formal derivation of programs , 1975, Commun. ACM.

[36]  Brigitte Plateau On the stochastic structure of parallelism and synchronization models for distributed algorithms , 1985, SIGMETRICS 1985.

[37]  Kevin Burrage,et al.  Stochastic approaches for modelling in vivo reactions , 2004, Comput. Biol. Chem..

[38]  Jane Hillston,et al.  Bio-PEPA: A framework for the modelling and analysis of biological systems , 2009, Theor. Comput. Sci..

[39]  Averill M. Law,et al.  Simulation Modeling and Analysis , 1982 .

[40]  Gianfranco Ciardo,et al.  Logic and stochastic modeling with S m A r T , 2006, Perform. Evaluation.

[41]  Roberto Gorrieri,et al.  Extended Markovian Process Algebra , 1996, CONCUR.

[42]  David M. Nicol,et al.  Fluid stochastic Petri nets: Theory, applications, and solution techniques , 1998, Eur. J. Oper. Res..

[43]  Masahiro Fujita,et al.  Multi-Terminal Binary Decision Diagrams: An Efficient Data Structure for Matrix Representation , 1997, Formal Methods Syst. Des..

[44]  Marco Ajmone Marsan,et al.  Modelling with Generalized Stochastic Petri Nets , 1995, PERV.

[45]  Peter J. Haas,et al.  Stochastic Petri Nets: Modelling, Stability, Simulation , 2002 .