-
1
-
-
17644364302
-
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
12
-
-
1342309249
-
Hybrid simulation of cellular behavior
-
Kiehl TR, Mattheyses RM, Simmons MK, Hybrid simulation of cellular behavior, Bioinformatics 20(3):316-322, 2004.
-
(2004)
Bioinformatics
, vol.20
, Issue.3
, pp. 316-322
-
-
Kiehl, T.R.1
Mattheyses, R.M.2
Simmons, M.K.3
-
13
-
-
0037109565
-
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
-
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
-
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
-
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
-
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
-
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
-
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
-
21
-
-
0033648431
-
Hybrid Petri net representation of gene regulatory network
-
Matsuno H, Doi A, Nagasaki M, Miyano S, Hybrid Petri net representation of gene regulatory network, in Proceedings of the 5th Pacific Symposium on Biocomputing 341-352, 2000.
-
(2000)
Proceedings of the 5th Pacific Symposium on Biocomputing
, pp. 341-352
-
-
Matsuno, H.1
Doi, A.2
Nagasaki, M.3
Miyano, S.4
-
22
-
-
0035888407
-
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
-
24
-
-
0036607144
-
Computational approaches for analysis of cis-regulatory networks
-
Brown CT, Rust AG, Clarke PJC, Pan Z, Schilstra MJ, Buysscher TD, Griffin G, Wold BJ, Cameron RA, Davidson EH, Bolouri H, Computational approaches for analysis of cis-regulatory networks, Dev Bio 246 86-102, 2002.
-
(2002)
Dev. Bio.
, vol.246
, pp. 86-102
-
-
Brown, C.T.1
Rust, A.G.2
Clarke, P.J.C.3
Pan, Z.4
Schilstra, M.J.5
Buysscher, T.D.6
Griffin, G.7
Wold, B.J.8
Cameron, R.A.9
Davidson, E.H.10
Bolouri, H.11
-
25
-
-
0033778277
-
Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis
-
Shimizu TS, Novère NL, Levin MD, Beavil AJ, Sutton BJ, Bray D, Molecular model of a lattice of signalling proteins involved in bacterial chemotaxis, Nature Cell Bio 2:792-796, 2000.
-
(2000)
Nature Cell Bio.
, vol.2
, pp. 792-796
-
-
Shimizu, T.S.1
Novère, N.L.2
Levin, M.D.3
Beavil, A.J.4
Sutton, B.J.5
Bray, D.6
-
26
-
-
0000896334
-
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
-
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
-
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
-
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
-
32
-
-
2942511481
-
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
-
-
Netx. Computer software, jnlp.sourceforge.net/netx
-
Maxwell JA, Netx. Computer software, jnlp.sourceforge.net/netx, 2003.
-
(2003)
-
-
Maxwell, J.A.1
-
34
-
-
12144272517
-
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
-
-
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
-
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
-
-
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
-
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
-
-
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
-
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
-
-
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
-
42
-
-
0037342537
-
The Systems Biology Markup Language (SBML): A medium for representation and exchange of biochemical network models
-
M Hucka, op. cit.
-
(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
-
43
-
-
0242490780
-
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
-
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
-
-
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
-
46
-
-
45149136906
-
Toward a universal random number generator
-
Marsaglia G, Zaman A, Tsang W-W, Toward a universal random number generator, Lett Stat Prob 9:35, 1990.
-
(1990)
Lett. Stat. Prob.
, vol.9
, pp. 35
-
-
Marsaglia, G.1
Zaman, A.2
Tsang, W.-W.3
-
47
-
-
0025503132
-
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
-
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
-
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
-
-
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
-
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
-
53
-
-
4143074525
-
Evolution of 'design' principles in biochemical networks
-
de Atauri P, Orrell D, Ramsey S, Bolouri H, Evolution of 'design' principles in biochemical networks, IEEE Sys Bio 1:28-40, 2004.
-
(2004)
IEEE Sys. Bio.
, vol.1
, pp. 28-40
-
-
de Atauri, P.1
Orrell, D.2
Ramsey, S.3
Bolouri, H.4
|