메뉴 건너뛰기




Volumn 3, Issue 2, 2005, Pages 437-454

Dizzy: Stochastic simulation of large-scale genetic regulatory networks (supplementary material)

Author keywords

[No Author keywords available]

Indexed keywords

GALACTOSE; MESSENGER RNA; TRANSCRIPTION FACTOR GAL4;

EID: 17644372713     PISSN: 02197200     EISSN: None     Source Type: Journal    
DOI: 10.1142/S0219720005001144     Document Type: Article
Times cited : (30)

References (54)
  • 1
    • 17644364302 scopus 로고    scopus 로고
    • Institute for Systems Biology, Seattle, WA, USA, Mar labs.systemsbiology.net/bolouri/software/Dizzy
    • Ramsey SA, Dizzy User Manual, Institute for Systems Biology, Seattle, WA, USA, Mar 2004. labs.systemsbiology.net/bolouri/software/Dizzy.
    • (2004) Dizzy User Manual
    • Ramsey, S.A.1
  • 2
    • 0036403704 scopus 로고    scopus 로고
    • Genetic 'Code': Representations and dynamical models of genetic components and networks
    • Gilman A, Arkin AP, Genetic 'Code': Representations and dynamical models of genetic components and networks, Annu Rev Genom Hum Genet 3:341-369, 2002.
    • (2002) Annu. Rev. Genom. Hum. Genet. , vol.3 , pp. 341-369
    • Gilman, A.1    Arkin, A.P.2
  • 3
    • 10044260032 scopus 로고    scopus 로고
    • Modeling and simulation of biochemical systems with stochasticity
    • Meng TC, Somani S, Dhar P, Modeling and simulation of biochemical systems with stochasticity, In Silico Bio 4:24, 2003.
    • (2003) In Silico Bio. , vol.4 , pp. 24
    • Meng, T.C.1    Somani, S.2    Dhar, P.3
  • 4
    • 14644425712 scopus 로고    scopus 로고
    • Toward computational systems biology
    • You L, Toward computational systems biology, Cell Biochem Biophys 40:1-18, 2004.
    • (2004) Cell Biochem. Biophys. , vol.40 , pp. 1-18
    • You, L.1
  • 5
    • 0017030517 scopus 로고
    • A general method for numerically simulating the stochastic time evolution of coupled chemical reactions
    • Gillespie DT, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, J Comp Phys 22:403-434, 1976.
    • (1976) J. Comp. Phys. , vol.22 , pp. 403-434
    • Gillespie, D.T.1
  • 6
    • 0001601301 scopus 로고
    • Stochastic approach to chemical kinetics
    • McQuarrie DA, Stochastic approach to chemical kinetics, J Appl Prob 4:413, 1967.
    • (1967) J. Appl. Prob. , vol.4 , pp. 413
    • McQuarrie, D.A.1
  • 7
    • 0001144902 scopus 로고    scopus 로고
    • Efficient exact stochastic simulation of chemical systems with many species and many channels
    • Gibson MA, Bruck J, Efficient exact stochastic simulation of chemical systems with many species and many channels, J Phys Chem A 104 1876-1889, 2000.
    • (2000) J. Phys. Chem. A , vol.104 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 8
    • 0032492834 scopus 로고    scopus 로고
    • Predicting temporal fluctuations in an intracellular signaling pathway
    • Morton-Firth CJ, Bray D, Predicting temporal fluctuations in an intracellular signaling pathway, J Theo Bio 192:117-128, 1998.
    • (1998) J. Theo. Bio. , vol.192 , pp. 117-128
    • Morton-Firth, C.J.1    Bray, D.2
  • 9
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting systems
    • Gillespie DT, Approximate accelerated stochastic simulation of chemically reacting systems, J Chem Phys 115(4):1716-1733, 2001.
    • (2001) J. Chem. Phys. , vol.115 , Issue.4 , pp. 1716-1733
    • Gillespie, D.T.1
  • 10
    • 0242425970 scopus 로고    scopus 로고
    • Improved leap-size selection for accelerated stochastic simulation
    • Gillespie DT, Petzold LR, Improved leap-size selection for accelerated stochastic simulation, J Chem Phys 119(16):8229-8234, 2003.
    • (2003) J. Chem. Phys. , vol.119 , Issue.16 , pp. 8229-8234
    • Gillespie, D.T.1    Petzold, L.R.2
  • 11
    • 1542345686 scopus 로고    scopus 로고
    • Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
    • Puchalka J, Kierzek AM, Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks, Biophys J 86:1357-1372, 2004.
    • (2004) Biophys. J. , vol.86 , pp. 1357-1372
    • Puchalka, J.1    Kierzek, A.M.2
  • 13
    • 0037109565 scopus 로고    scopus 로고
    • Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics
    • Haseltine EL, Rawlings JB, Approximate simulation of coupled fast and slow reactions for stochastic chemical kinetics, J Chem Phys 117 6959-6969, 2002.
    • (2002) J. Chem. Phys. , vol.117 , pp. 6959-6969
    • Haseltine, E.L.1    Rawlings, J.B.2
  • 14
    • 0347724159 scopus 로고    scopus 로고
    • Adaptive stochastic-deterministic chemical kinetic simulations
    • Vasudeva K, Bhalla US, Adaptive stochastic-deterministic chemical kinetic simulations, Bioinformatics 20(l):78-84, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.1 , pp. 78-84
    • Vasudeva, K.1    Bhalla, U.S.2
  • 16
    • 1542400036 scopus 로고    scopus 로고
    • A multi-algorithm, multi-timescale method for cell simulation
    • Takahashi K et al., A multi-algorithm, multi-timescale method for cell simulation, Bioinformatics 20(4):538-546, 2004.
    • (2004) Bioinformatics , vol.20 , Issue.4 , pp. 538-546
    • Takahashi, K.1
  • 17
    • 0034225547 scopus 로고    scopus 로고
    • The chemical Langevin equation
    • Gillespie DT, The chemical Langevin equation, J Chem Phys 113 297-306, 2000.
    • (2000) J. Chem. Phys. , vol.113 , pp. 297-306
    • Gillespie, D.T.1
  • 18
    • 0035193294 scopus 로고    scopus 로고
    • Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations
    • Kepler TB, Elston TC, Stochasticity in transcriptional regulation: Origins, consequences, and mathematical representations, Biophys J 81:3116-3136, 2001.
    • (2001) Biophys. J. , vol.81 , pp. 3116-3136
    • Kepler, T.B.1    Elston, T.C.2
  • 19
    • 0037444724 scopus 로고    scopus 로고
    • Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
    • Rao CV, Arkin AP, Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm, J Chem Phys 118(11):4999-5010, 2003.
    • (2003) J. Chem. Phys. , vol.118 , Issue.11 , pp. 4999-5010
    • Rao, C.V.1    Arkin, A.P.2
  • 20
    • 0032499741 scopus 로고    scopus 로고
    • Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets
    • Goss PJ, Peccoud J, Quantitative modeling of stochastic systems in molecular biology by using stochastic Petri nets, Proc Nat Acad Sci USA 95:6750-6755, 1998.
    • (1998) Proc. Nat. Acad. Sci. USA , vol.95 , pp. 6750-6755
    • Goss, P.J.1    Peccoud, J.2
  • 22
    • 0035888407 scopus 로고    scopus 로고
    • Application of a stochastic name-passing calculus to representation and simulation of molecular processes
    • Priami C et al., Application of a stochastic name-passing calculus to representation and simulation of molecular processes, Inf Proc Lett 80:25-31, 2001.
    • (2001) Inf. Proc. Lett. , vol.80 , pp. 25-31
    • Priami, C.1
  • 26
    • 0000896334 scopus 로고    scopus 로고
    • Numerical approach to fast reactions in reaction-diffusion systems: Application to buffered calcium waves in bistable models
    • Slepchenko BM, Schaff JC, Choi YS, Numerical approach to fast reactions in reaction-diffusion systems: Application to buffered calcium waves in bistable models, J Comp Phys 162:186-218, 2000.
    • (2000) J. Comp. Phys. , vol.162 , pp. 186-218
    • Slepchenko, B.M.1    Schaff, J.C.2    Choi, Y.S.3
  • 27
    • 0002675486 scopus 로고    scopus 로고
    • Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes
    • Bower JM (ed.), Plenum, New York
    • Stiles JR, Monte Carlo simulation of neurotransmitter release using MCell, a general simulator of cellular physiological processes, in Bower JM (ed.), Computational Neuroscience, pp. 279-284, Plenum, New York, 1998.
    • (1998) Computational Neuroscience , pp. 279-284
    • Stiles, J.R.1
  • 29
    • 17644397436 scopus 로고    scopus 로고
    • GNU lesser general public license
    • Computer software license agreement, Free Software Foundation, www.gnu.org/copyleft
    • Stallman R, GNU lesser general public license. Computer software license agreement, Free Software Foundation, www.gnu.org/copyleft, 1999.
    • (1999)
    • Stallman, R.1
  • 30
    • 0003838194 scopus 로고    scopus 로고
    • The evolution of numerical computing in Java
    • java.sun.com/people/jag/FP.html
    • Gosling J, The evolution of numerical computing in Java, java.sun.com/people/jag/FP.html, 1997.
    • (1997)
    • Gosling, J.1
  • 31
  • 32
    • 2942511481 scopus 로고    scopus 로고
    • Introduction to the systems biology workbench
    • tech. rep., JST ERATO Kitano Symbiotic Systems Project, May
    • Hucka M, Finney A, Sauro H, Bolouri H, Introduction to the systems biology workbench, tech. rep., JST ERATO Kitano Symbiotic Systems Project, May, 2001.
    • (2001)
    • Hucka, M.1    Finney, A.2    Sauro, H.3    Bolouri, H.4
  • 33
    • 17644392341 scopus 로고    scopus 로고
    • Netx. Computer software, jnlp.sourceforge.net/netx
    • Maxwell JA, Netx. Computer software, jnlp.sourceforge.net/netx, 2003.
    • (2003)
    • Maxwell, J.A.1
  • 34
    • 12144272517 scopus 로고    scopus 로고
    • Java network launching protocol & API specification
    • Tech. Rep. JSR-56, Sun Microsystems, May
    • Schmidt R, Java network launching protocol&API specification, Tech. Rep. JSR-56, Sun Microsystems, May, 2001.
    • (2001)
    • Schmidt, R.1
  • 35
    • 17644388708 scopus 로고    scopus 로고
    • JavaHelp 2.0 specification, Tech. Rep. JSR-097, Sun Microsystems, Mar
    • Brinkley R, JavaHelp 2.0 specification, Tech. Rep. JSR-097, Sun Microsystems, Mar 2003.
    • (2003)
    • Brinkley, R.1
  • 36
    • 0004010787 scopus 로고    scopus 로고
    • JAMA: A Java matrix package
    • Computer software, math.nist.gov/javanumerics/jama
    • Boisvert RF et al., JAMA: A Java matrix package. Computer software, math.nist.gov/javanumerics/jama, 1999.
    • (1999)
    • Boisvert, R.F.1
  • 37
    • 17644426252 scopus 로고    scopus 로고
    • CERN Colt software package. Computer software, European Center for Nuclear Research, hoschek.home.cern.ch/hoschek/colt, Nov
    • Hoschek W, CERN Colt software package. Computer software, European Center for Nuclear Research, hoschek.home.cern.ch/hoschek/colt, Nov 2002.
    • (2002)
    • Hoschek, W.1
  • 38
    • 17644403027 scopus 로고    scopus 로고
    • Implementing Runge-Kutta solvers in Java
    • tech. rep., Acadia University, Honors Undergraduate Thesis, Jodrey School of Computer Science
    • Patterson MD, Implementing Runge-Kutta solvers in Java, tech. rep., Acadia University, 2002. Honors Undergraduate Thesis, Jodrey School of Computer Science.
    • (2002)
    • Patterson, M.D.1
  • 39
    • 17644379838 scopus 로고    scopus 로고
    • OdeToJava. Computer software, Dalhousie University, Halifax, NS, Canada, www.netlib.org/ode
    • Patterson MD, Spiteri RJ, OdeToJava. Computer software, Dalhousie University, Halifax, NS, Canada, www.netlib.org/ode, 2002.
    • (2002)
    • Patterson, M.D.1    Spiteri, R.J.2
  • 40
    • 0037342537 scopus 로고    scopus 로고
    • The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models
    • Hucka M, Finney A, Sauro HM, Bolouri H, Doyle JC, Kitano H et al. The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models, Bioinformatics 19(4):524-531, 2003.
    • (2003) Bioinformatics , vol.19 , Issue.4 , pp. 524-531
    • Hucka, M.1    Finney, A.2    Sauro, H.M.3    Bolouri, H.4    Doyle, J.C.5    Kitano, H.6
  • 41
    • 17644378299 scopus 로고    scopus 로고
    • SBMLValidate. Computer software, JST ERATO Kitano Symbiotic Systems Project, California Institute of Technology, USA, sbw.sourceforge.net/sbw/software, Distributed with the Systems Biology Workbench
    • Sauro H et al., SBMLValidate. Computer software, JST ERATO Kitano Symbiotic Systems Project, California Institute of Technology, USA, sbw.sourceforge.net/sbw/software, 2003.Distributed with the Systems Biology Workbench
    • (2003)
    • Sauro, H.1
  • 43
    • 0242490780 scopus 로고    scopus 로고
    • Cytoscape: A software environment for integrated models of biomolecular interaction networks
    • Shannon P et al., Cytoscape: A software environment for integrated models of biomolecular interaction networks, Genome Res 13:2498-2504, 2003.
    • (2003) Genome Res. , vol.13 , pp. 2498-2504
    • Shannon, P.1
  • 44
    • 17644370898 scopus 로고    scopus 로고
    • RngPack: High quality random numbers for Java
    • Computer software distributed through the CERN Colt library
    • Houle P, RngPack: High quality random numbers for Java. Computer software distributed through the CERN Colt library
    • Houle, P.1
  • 45
    • 17644424872 scopus 로고    scopus 로고
    • CERN Colt software package. Computer software, European Center for Nuclear Research, hoschek.home.cern.ch/hoschek/colt, Nov
    • W Hoschek, op cit 2002.
    • (2002)
    • Hoschek, W.1
  • 47
    • 0025503132 scopus 로고
    • A review of pesudorandom number generators
    • James F, A review of pesudorandom number generators, Comp Phys Comm 60:329-344, 1990.
    • (1990) Comp. Phys. Comm. , vol.60 , pp. 329-344
    • James, F.1
  • 48
    • 0001442051 scopus 로고
    • Issues in the numerical solution of evolutionary delay differential equations
    • Baker CTH, Paul CAH, Willé DR, Issues in the numerical solution of evolutionary delay differential equations, Adv Comp Math 3 171-196, 1995.
    • (1995) Adv. Comp. Math. , vol.3 , pp. 171-196
    • Baker, C.T.H.1    Paul, C.A.H.2    Willé, D.R.3
  • 49
    • 0000619830 scopus 로고
    • Some properties of beta and gamma distributions
    • Jambunathan MV, Some properties of beta and gamma distributions, Ann Math Stat 25:401-405, 1954.
    • (1954) Ann. Math. Stat. , vol.25 , pp. 401-405
    • Jambunathan, M.V.1
  • 51
    • 0004161838 scopus 로고
    • New Rochelle, NY, USA: Cambridge University Press
    • Press WH et al., Numerical Recipes in C. New Rochelle, NY, USA: Cambridge University Press, 1988.
    • (1988) Numerical Recipes in C
    • Press, W.H.1
  • 52
    • 0035812883 scopus 로고    scopus 로고
    • Stochastic kinetic analysis of the Escherichia coli stress circuit using σ(32)-targeted antisense
    • Srivastava R, Peterson MS, Bentley WE, Stochastic kinetic analysis of the Escherichia coli stress circuit using σ(32)-targeted antisense, Biotech Bioeng 75:120-129, 2001.
    • (2001) Biotech. Bioeng. , vol.75 , pp. 120-129
    • Srivastava, R.1    Peterson, M.S.2    Bentley, W.E.3


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.