CERENA: ChEmical REaction network analyzer-a toolbox for the simulation and analysis of stochastic chemical kinetics

PLoS ONE

Volumn 11, Issue 1, 2016, Pages

  Kazeroonian, Atefeh ^a,b   Fröhlich, Fabian ^a,b   Raue, Andreas ^c   Theis, Fabian J ^a,b   Hasenauer, Jan ^a,b  

^a INSTITUTE OF EPIDEMIOLOGY   (Germany)

^b TECHNICAL UNIVERSITY OF MUNICH   (Germany)

^c MERRIMACK PHARMACEUTICALS   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ALGORITHM; BIOLOGICAL MODEL; COMPUTER SIMULATION; KINETICS; MARKOV CHAIN; PHYSIOLOGY; SIGNAL TRANSDUCTION; SOFTWARE;

ALGORITHMS; COMPUTER SIMULATION; KINETICS; MODELS, BIOLOGICAL; SIGNAL TRANSDUCTION; SOFTWARE; STOCHASTIC PROCESSES;

EID: 84988516464     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0146732     Document Type: Article

References (41)

1. van Kampen NG. Stochastic processes in physics and chemistry. 3rd ed. Amsterdam: North-Holland; 2007.
2. Gillespie DT. Exact stochastic simulation of coupled chemical reactions. J Phys Chem. 1977 Dec; 81(25):2340-2361. doi: 10.1021/j100540a008
3. Shahrezaei V, Swain PS. Analytical distributions for stochastic gene expression. Proc Natl Acad Sci U S A. 2008 Nov; 105(45):17256-17261. doi: 10.1073/pnas.0803850105 PMID: 18988743
4. Ramaswamy R, González-Segredo N, Sbalzarini I, Grima R. Discreteness-induced concentration inversion in mesoscopic chemical systems. Nat Comm. 2012 Apr; 3(779).
5. Eldar A, Elowitz MB. Functional roles for noise in genetic circuits. Nature. 2010 Sept; 467(9):1-7.
6. Gillespie DT. A rigorous derivation of the chemical master equation. Physica A. 1992 Sept; 188(1): 404-425. doi: 10.1016/0378-4371(92)90283-V
7. Jahnke T, Huisinga W. Solving the chemical master equation for monomolecular reaction systems analytically. J Math Biol. 2007 Jan; 54(1):1-26. doi: 10.1007/s00285-006-0034-x PMID: 16953443
8. Munsky B, Khammash M. The finite state projection algorithm for the solution of the chemical master equation. J Chem Phys. 2006 Jan; 124(4):044104. doi: 10.1063/1.2145882 PMID: 16460146
9. Mateescu M, Wolf V, Didier F, Henzinger TA. Fast adaptive uniformisation of the chemical master equation. IET Syst Biol. 2010; 4(6):441-452. doi: 10.1049/iet-syb.2010.0005 PMID: 21073242
10. Kazeev V, Khammash M, Nip M, Schwab C. Direct solution of the Chemical Master Equation using quantized tensor trains. PLOS Comput Biol. 2014 Mar; 10(3):e1003359. doi: 10.1371/journal.pcbi. 1003359 PMID: 24626049
11. Engblom S. Computing the moments of high dimensional solutions of the master equation. Appl Math Comp. 2006; 180:498-515. doi: 10.1016/j.amc.2005.12.032
12. Grima R. An effective rate equation approach to reaction kinetics in small volumes: Theory and application to biochemical reactions in nonequilibrium steady-state conditions. J Chem Phys. 2010 July; 133(035101).
13. Hasenauer J, Wolf V, Kazeroonian A, Theis FJ. Method of conditional moments (MCM) for the chemical master equation. J Math Biol. 2014 Aug; 69(3):687-735. doi: 10.1007/s00285-013-0711-5 PMID: 23918091
14. Thomas P, Popovic N, Grima R. Phenotypic switching in gene regulatory networks. Proc Natl Acad Sci U S A. 2014 May; 111(19):6994-6999. doi: 10.1073/pnas.1400049111 PMID: 24782538
15. Zechner C, Ruess J, Krenn P, Pelet S, Peter M, Lygeros J, et al. Moment-based inference predicts bimodality in transient gene expression. Proc Natl Acad Sci U S A. 2012 May; 109(21):8340-8345. doi: 10.1073/pnas.1200161109 PMID: 22566653
16. Milner P, Gillespie CS, Wilkinson DJ. Moment closure based parameter inference of stochastic kinetic models. Stat Comp. 2013 Mar; 23(2):287-295. doi: 10.1007/s11222-011-9310-8
17. Raue A, Schilling M, Bachmann J, Matteson A, Schelke M, Kaschek D, et al. Lessons learned from quantitative dynamical modeling in systems biology. PLOS ONE. 2013 Sept; 8(9):e74335. doi: 10. 1371/journal.pone.0074335 PMID: 24098642
18. Sanft KR, Wu S, Roh M, Fu J, Lim RK, Petzold LR. StochKit2: software for discrete stochastic simulation of biochemical systems with events. Bioinf. 2011; 27(17):2457-2458. doi: 10.1093/bioinformatics/btr401
19. Maarleveld TR, Olivier BG, Bruggeman FJ. StochPy: A comprehensive, user-friendly tool for simulating stochastic biological processes. PLOS ONE. 2013 11; 8(11):e79345. doi: 10.1371/journal.pone. 0079345 PMID: 24260203
20. Ramsey S, Orrell D, Bolouri H. Dizzy: stochastic simulation of large-scale genetic regulatory networks. J Bioinform Comput Biol. 2005 Apr; 3(2):415-436. doi: 10.1142/S0219720005001144 PMID: 15852513
21. Hegland M, Fletcher-Costin R. CmePy documentation. http://fcostin.github.com/cmepy; 2010.
22. Hoops S, Sahle S, Gauges R, Lee C, Pahle J, Simus N, et al. COPASI-a COmplex PAthway SImulator. Bioinf. 2006; 22:3067-3074. doi: 10.1093/bioinformatics/btl485
23. Gillespie CS. Moment-closure approximations for mass-action models. IET Syst Biol. 2009 Jan; 3(1): 52-58. doi: 10.1049/iet-syb:20070031 PMID: 19154084
24. Hespanha J. Moment closure for biochemical networks. In: Proc. Int. Symp. on Communications, Control and Signal Processing; 2008. p. 42-147.
25. Schnoerr D, Sanguinetti G, Grima R. Comparison of different moment-closure approximations for stochastic chemical kinetics. The Journal of Chemical Physics. 2015; 143(18). doi: 10.1063/1.4934990 PMID: 26567686
26. Thomas P, Matuschek H, Grima R. Intrinsic Noise Analyzer: A software package for the exploration of stochastic biochemical kinetics using the system size expansion. PLOS ONE. 2013 Jun; 7(6):e38518. doi: 10.1371/journal.pone.0038518
27. Lapin M, Mikeev L, Wolf V. SHAVE: Stochastic Hybrid Analysis of Markov Population Models. In: Proceedings of the 14th International Conference on Hybrid Systems: Computation and Control. HSCC'11. New York, NY, USA: ACM; 2011. p. 311-312. Available from: http://doi.acm.org/10.1145/1967701.1967746.
28. Anderson DF. A modified next reaction method for simulating chemical systems with time dependent propensities and delays. J Chem Phys. 2007 Dec; 127(214107). PMID: 18067349
29. Norris JR. Continuous-time Markov chains I. In: Markov Chains. Cambridge University Press; 1997. p. 60-107. Cambridge Books Online.
30. Grima R. Linear-noise approximation and the chemical master equation agree up to second-order moments for a class of chemical systems. Phys Rev E. 2015 Oct; 92:042124. doi: 10.1103/PhysRevE. 92.042124
31. Singh A, Hespanha JP. Approximate moment dynamics for chemically reacting systems. IEEE Trans Autom Control. 2011 Feb; 56(2):414-418. doi: 10.1109/TAC.2010.2088631
32. Hindmarsh AC, Brown PN, Grant KE, Lee SL, Serban R, Shumaker DE, et al. SUNDIALS: Suite of Nonlinear and Differential/Algebraic Equation Solvers. ACM T Math Software. 2005 Sept; 31(3):363-396. doi: 10.1145/1089014.1089020
33. Kazeroonian A, Theis FJ, Hasenauer J. Modeling of stochastic biological processes with non-polynomial propensities using non-central conditional moment equation. In: Proc. of the 19th IFACWorld Congress. vol. 19. Cape Town, South Africa; 2014. p. 1729-1735.
34. Raue A, Steiert B, Schelker M, Kreutz C, Maiwald T, Hass H, et al. Data2Dynamics: a modeling environment tailored to parameter estimation in dynamical systems. Bioinformatics. 2015 Jul.
35. Raue A, Kreutz C, Maiwald T, Bachmann J, Schilling M, Klingmüller U, et al. Structural and practical identifiability analysis of partially observed dynamical models by exploiting the profile likelihood. Bioinf. 2009 May; 25(25):1923-1929. doi: 10.1093/bioinformatics/btp358
36. Swameye I, Müller TG, Timmer J, Sandra O, Klingmüller U. Identification of nucleocytoplasmic cycling as a remote sensor in cellular signaling by databased modeling. Proc Natl Acad Sci USA. 2003 Feb; 100(3):1028-1033. doi: 10.1073/pnas.0237333100 PMID: 12552139
37. Fröhlich F, Thomas P, Kazeroonian A, Theis FJ, Grima R, Hasenauer J. Inference for stochastic chemical kinetics using moment equations and system size expansion. submitted. 2015.
38. Hasenauer J, Hasenauer C, Hucho T, Theis FJ. ODE constrained mixture modelling: A method for unraveling subpopulation structures and dynamics. PLOS Comput Biol. 2014 July; 10(7):e1003686. doi: 10.1371/journal.pcbi.1003686 PMID: 24992156
39. Thomas P, Grima R. Approximate probability distributions of the master equation. Phys Rev E. 2015 Jul; 92:012120. doi: 10.1103/PhysRevE.92.012120
40. Andreychenko A, Mikeev L, Wolf V. Reconstruction of multimodal distributions for hybrid momentbased chemical kinetics. Journal of Coupled Systems and Multiscale Dynamics. 2015-06-01T00:00:00; 3(2):156-163. doi: 10.1166/jcsmd.2015.1073
41. Andreychenko A, Bortolussi L, Grima R, Thomas P and Wolf V. Distribution approximations for the chemical master equation: comparison of the method of moments and the system size expansion. submitted. 2015.