-
1
-
-
0037444724
-
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
-
Arkin A.P., and Rao C.V. Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm. Journal of Chemical Physics 11 (2003) 4999-5010
-
(2003)
Journal of Chemical Physics
, vol.11
, pp. 4999-5010
-
-
Arkin, A.P.1
Rao, C.V.2
-
2
-
-
84957369657
-
Verifying continuous time Markov chains
-
Proc. 8th International Conference on Computer Aided Verification. CAV'96, Springer
-
Aziz A., Kanwal K., Singhal V., and Brayton V. Verifying continuous time Markov chains. Proc. 8th International Conference on Computer Aided Verification. CAV'96. LNCS vol. 1102 (1996), Springer 269-276
-
(1996)
LNCS
, vol.1102
, pp. 269-276
-
-
Aziz, A.1
Kanwal, K.2
Singhal, V.3
Brayton, V.4
-
3
-
-
10644250404
-
Evolving a Lingua Franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project
-
Bornstein B.J., Doyle J.C., Finney A., Funahashi A., Hucka M., Keating S.M., Kitano H., Kovitz B.L., Matthews J., Shapiro B.E., and Schilstra M.J. Evolving a Lingua Franca and associated software infrastructure for computational systems biology: The systems biology markup language (SBML) project. Systems Biology 1 (2004) 41-53
-
(2004)
Systems Biology
, vol.1
, pp. 41-53
-
-
Bornstein, B.J.1
Doyle, J.C.2
Finney, A.3
Funahashi, A.4
Hucka, M.5
Keating, S.M.6
Kitano, H.7
Kovitz, B.L.8
Matthews, J.9
Shapiro, B.E.10
Schilstra, M.J.11
-
5
-
-
43049179364
-
Modeling biological systems in stochastic concurrent constraint programming
-
Bortolussi L., and Policriti A. Modeling biological systems in stochastic concurrent constraint programming. Constraints 13 1 (2008)
-
(2008)
Constraints
, vol.13
, Issue.1
-
-
Bortolussi, L.1
Policriti, A.2
-
6
-
-
34548268951
-
Stochastic concurrent constraint programming and differential equations
-
Proc. of 5th International Workshop of Quantitative Aspects of Programming Languages. QAPL 2007
-
Bortolussi L., and Policriti A. Stochastic concurrent constraint programming and differential equations. Proc. of 5th International Workshop of Quantitative Aspects of Programming Languages. QAPL 2007. ENTCS vol. 16713 (2007)
-
(2007)
ENTCS
, vol.16713
-
-
Bortolussi, L.1
Policriti, A.2
-
7
-
-
67650081719
-
Constraint-based approaches to stochastic dynamics of biological systems
-
L. Bortolussi, Constraint-based approaches to stochastic dynamics of biological systems, University of Udine Ph.D. Thesis Series, CS2007/1, 2007
-
University of Udine Ph.D. Thesis Series
, vol.CS2007 1
, pp. 2007
-
-
Bortolussi, L.1
-
8
-
-
45749113795
-
Hybrid systems and biology
-
Springer (Chapter for the Tutorial of SFM-08:Bio)
-
Bortolussi L., and Policriti A. Hybrid systems and biology. LNCS vol. 5015 (2008), Springer 424-448 (Chapter for the Tutorial of SFM-08:Bio)
-
(2008)
LNCS
, vol.5015
, pp. 424-448
-
-
Bortolussi, L.1
Policriti, A.2
-
10
-
-
33746062738
-
Automatically deriving ODEs from process algebra models of signalling pathways
-
M. Calder, S. Gilmore, J. Hillston, Automatically deriving ODEs from process algebra models of signalling pathways, in: Proc. of CMSB'05, 2005, pp. 204-215
-
(2005)
Proc. of CMSB'05
, pp. 204-215
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
11
-
-
38549120134
-
Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA
-
Proc. of Bionconcur'04, Springer Extended version in T. Comp. Sys. Biology VII
-
Calder M., Gilmore S., and Hillston J. Modelling the influence of RKIP on the ERK signalling pathway using the stochastic process algebra PEPA. Proc. of Bionconcur'04. LNCS vol. 4230 (2006), Springer 1-23 Extended version in T. Comp. Sys. Biology VII
-
(2006)
LNCS
, vol.4230
, pp. 1-23
-
-
Calder, M.1
Gilmore, S.2
Hillston, J.3
-
12
-
-
33845200552
-
Stronger computational modelling of signalling pathways using both continuous and discrete-space methods
-
Proc. of CMSB'06, Springer
-
Calder M., Duguid A., Gilmore S., and Hillston J. Stronger computational modelling of signalling pathways using both continuous and discrete-space methods. Proc. of CMSB'06. LNCS vol. 4210 (2006), Springer 63-77
-
(2006)
LNCS
, vol.4210
, pp. 63-77
-
-
Calder, M.1
Duguid, A.2
Gilmore, S.3
Hillston, J.4
-
13
-
-
33845385005
-
Analysis of signalling pathways using continuous time Markov chains
-
T. Comp. Sys. Biology VI, Springer
-
Calder M., Vyshemirsky V., Gilbert D., and Orton R. Analysis of signalling pathways using continuous time Markov chains. T. Comp. Sys. Biology VI. LNCS vol. 4220 (2006), Springer 44-67
-
(2006)
LNCS
, vol.4220
, pp. 44-67
-
-
Calder, M.1
Vyshemirsky, V.2
Gilbert, D.3
Orton, R.4
-
14
-
-
33846185710
-
Accelerated stochastic simulation of the stiff enzyme-substrate reaction
-
Cao Y., Gillespie D.T., and Petzold L. Accelerated stochastic simulation of the stiff enzyme-substrate reaction. Journal of Chemical Physics 123 14 (2005) 144917-144929
-
(2005)
Journal of Chemical Physics
, vol.123
, Issue.14
, pp. 144917-144929
-
-
Cao, Y.1
Gillespie, D.T.2
Petzold, L.3
-
15
-
-
41149144239
-
Approximate symbolic model checking of continuous-time Markov chains
-
Proceedings of CONCUR'99, Springer
-
Baier C., Katoen J.-P., and Hermanns H. Approximate symbolic model checking of continuous-time Markov chains. Proceedings of CONCUR'99. LNCS vol. 1664 (1999), Springer 146-161
-
(1999)
LNCS
, vol.1664
, pp. 146-161
-
-
Baier, C.1
Katoen, J.-P.2
Hermanns, H.3
-
16
-
-
4444383325
-
BioAmbients: An abstraction for biological compartments
-
Cardelli L., Panina E.M., Regev A., Shapiro E., and Silverman W. BioAmbients: An abstraction for biological compartments. Theoretical Computer Science 325 1 (2004) 141-167
-
(2004)
Theoretical Computer Science
, vol.325
, Issue.1
, pp. 141-167
-
-
Cardelli, L.1
Panina, E.M.2
Regev, A.3
Shapiro, E.4
Silverman, W.5
-
18
-
-
45749106370
-
A framework for the modelling and analysis of biological systems
-
Technical report EDI-INF-RR-1231, University of Edinburgh
-
F. Ciocchetta, J. Hillston, Bio-PEPA: A framework for the modelling and analysis of biological systems, Technical report EDI-INF-RR-1231, University of Edinburgh, 2008
-
(2008)
-
-
Ciocchetta, F.1
Hillston, J.2
PEPA, B.3
-
19
-
-
43049179364
-
Bio-PEPA: An extension of the process algebra PEPA for biochemical networks
-
Proc. of FBTC 2007
-
Ciocchetta F., and Hillston J. Bio-PEPA: An extension of the process algebra PEPA for biochemical networks. Proc. of FBTC 2007. ENTCS vol. 194(3) (2008) 103-117
-
(2008)
ENTCS
, vol.194 3
, pp. 103-117
-
-
Ciocchetta, F.1
Hillston, J.2
-
20
-
-
67650089028
-
-
F. Ciocchetta, S. Gilmore, M.L. Guerriero, J. Hillston, Integrated simulation and model-checking for the analysis of biochemical systems, in: Proc. of PASM 2008, in: ENTCS (in press)
-
F. Ciocchetta, S. Gilmore, M.L. Guerriero, J. Hillston, Integrated simulation and model-checking for the analysis of biochemical systems, in: Proc. of PASM 2008, in: ENTCS (in press)
-
-
-
-
21
-
-
58149293181
-
Modelling biological compartments in Bio-PEPA
-
Proc. of MeCBIC 2008
-
Ciocchetta F., and Guerriero M.L. Modelling biological compartments in Bio-PEPA. Proc. of MeCBIC 2008. ENTCS vol. 227 (2009) 77-95
-
(2009)
ENTCS
, vol.227
, pp. 77-95
-
-
Ciocchetta, F.1
Guerriero, M.L.2
-
22
-
-
60449103324
-
-
F. Ciocchetta, A. Degasperi, J. Hillston, M. Calder, Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA, in: Proc. of FBTC 2008, in: Electronic Notes in Theoretical Computer Science (ENTCS), 229 (1), 2009, pp. 145-163
-
F. Ciocchetta, A. Degasperi, J. Hillston, M. Calder, Some investigations concerning the CTMC and the ODE model derived from Bio-PEPA, in: Proc. of FBTC 2008, in: Electronic Notes in Theoretical Computer Science (ENTCS), vol. 229 (1), 2009, pp. 145-163
-
-
-
-
23
-
-
34250811943
-
Biological transactions for quantitative models
-
Proc. of MeCBIC 2006
-
Ciocchetta F., and Priami C. Biological transactions for quantitative models. Proc. of MeCBIC 2006. ENTCS 171(2) (2007) 55-67
-
(2007)
ENTCS
, vol.171 2
, pp. 55-67
-
-
Ciocchetta, F.1
Priami, C.2
-
24
-
-
67650302251
-
The BlenX Language with Biological Transactions
-
Trans. on Comput. Syst. Biol. IX, Springer
-
Ciocchetta F. The BlenX Language with Biological Transactions. Trans. on Comput. Syst. Biol. IX. LNBI vol. 5121 (2008), Springer
-
(2008)
LNBI
, vol.5121
-
-
Ciocchetta, F.1
-
25
-
-
37149036234
-
Modeling Kohn interaction maps with beta-binders: An example
-
Springer
-
Ciocchetta F., Priami C., and Quaglia P. Modeling Kohn interaction maps with beta-binders: An example. T. Comp. Sys. Biology. III (2005), Springer 33-48
-
(2005)
T. Comp. Sys. Biology. III
, pp. 33-48
-
-
Ciocchetta, F.1
Priami, C.2
Quaglia, P.3
-
26
-
-
34250812291
-
Language modeling and simulation of autoreactive lymphocytes recruitment in inflamed brain vessels
-
Costantin G., Laudanna C., Lecca P., Priami C., Quaglia P., and Rossi B. Language modeling and simulation of autoreactive lymphocytes recruitment in inflamed brain vessels. SIMULATION: Transactions of The Society for Modeling and Simulation International 80 (2003) 273-288
-
(2003)
SIMULATION: Transactions of The Society for Modeling and Simulation International
, vol.80
, pp. 273-288
-
-
Costantin, G.1
Laudanna, C.2
Lecca, P.3
Priami, C.4
Quaglia, P.5
Rossi, B.6
-
28
-
-
38149083357
-
Ruled-based modelling of cellular signalling
-
Proc. of CONCUR'07, Springer
-
Danos V., Feret J., Fontana W., Harmer R., and Krivine J. Ruled-based modelling of cellular signalling. Proc. of CONCUR'07. LNCS vol. 4703 (2007), Springer
-
(2007)
LNCS
, vol.4703
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Harmer, R.4
Krivine, J.5
-
29
-
-
49249102346
-
Scalable simulation of cellular signalling networks
-
V. Danos, J. Feret, W. Fontana, J. Krivine, Scalable simulation of cellular signalling networks, in: Proc. of APLAS'07, 2007
-
(2007)
Proc. of APLAS'07
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Krivine, J.4
-
30
-
-
40549119812
-
Abstract interpretation of reachable complexes in biological signalling networks
-
in: Proc. of VMCAI'08, Springer
-
V. Danos, J. Feret, W. Fontana, J. Krivine, Abstract interpretation of reachable complexes in biological signalling networks, in: Proc. of VMCAI'08, in: LNCS, Springer, 2008, pp. 83-97, http://dx.doi.org/10.1007/978-3-540-78163-9_11
-
(2008)
LNCS
, pp. 83-97
-
-
Danos, V.1
Feret, J.2
Fontana, W.3
Krivine, J.4
-
33
-
-
45749111042
-
The BlenX language: A tutorial
-
Springer (Chapter for the Tutorial of SFM-08:Bio)
-
Dematté L., Priami C., and Romanel A. The BlenX language: A tutorial. LNCS vol. 5015 (2008), Springer 313-365 (Chapter for the Tutorial of SFM-08:Bio)
-
(2008)
LNCS
, vol.5015
, pp. 313-365
-
-
Dematté, L.1
Priami, C.2
Romanel, A.3
-
34
-
-
0036212767
-
Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors
-
Eichler-Jonsson C., Gilles E.D., Muller G., and Schoeberl B. Computational modeling of the dynamics of the MAP kinase cascade activated by surface and internalized EGF receptors. Nature Biotechnology 20 (2002) 370-375
-
(2002)
Nature Biotechnology
, vol.20
, pp. 370-375
-
-
Eichler-Jonsson, C.1
Gilles, E.D.2
Muller, G.3
Schoeberl, B.4
-
35
-
-
49249084626
-
Relating continuous and discrete PEPA models of signalling pathways
-
Geisweiller N., Hillston J., and Stenico M. Relating continuous and discrete PEPA models of signalling pathways. Theoretical Computer Science 404 1-2 (2008) 97-111
-
(2008)
Theoretical Computer Science
, vol.404
, Issue.1-2
, pp. 97-111
-
-
Geisweiller, N.1
Hillston, J.2
Stenico, M.3
-
36
-
-
33645429016
-
Exact stochastic simulation of coupled chemical reactions
-
Gillespie D.T. Exact stochastic simulation of coupled chemical reactions. Journal of Physical Chemistry 81 (1977) 2340-2361
-
(1977)
Journal of Physical Chemistry
, vol.81
, pp. 2340-2361
-
-
Gillespie, D.T.1
-
37
-
-
38649122071
-
Probabilistic model checking of complex biological pathways
-
(special issue on Converging Sciences: Informatics and Biology)
-
Heath J., Kwiatkowska M., Norman G., Parker D., and Tymchyshyn O. Probabilistic model checking of complex biological pathways. Theoretical Computer Science 391 (2008) 239-257 (special issue on Converging Sciences: Informatics and Biology)
-
(2008)
Theoretical Computer Science
, vol.391
, pp. 239-257
-
-
Heath, J.1
Kwiatkowska, M.2
Norman, G.3
Parker, D.4
Tymchyshyn, O.5
-
39
-
-
0030921594
-
A database for post-genome analysis
-
Kanehisa M. A database for post-genome analysis. Trends in Genetics 13 (1997) 375-376
-
(1997)
Trends in Genetics
, vol.13
, pp. 375-376
-
-
Kanehisa, M.1
-
40
-
-
67650067791
-
-
KEGG home page. Available at
-
KEGG home page. Available at http://sbml.org/kegg2sbml.html
-
-
-
-
41
-
-
1542345686
-
Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks
-
Kierzek A.M., and Puchalka J. Bridging the gap between stochastic and deterministic regimes in the kinetic simulations of the biochemical reaction networks. Biophysical Journal 86 (2004) 1357-1372
-
(2004)
Biophysical Journal
, vol.86
, pp. 1357-1372
-
-
Kierzek, A.M.1
Puchalka, J.2
-
42
-
-
38149103597
-
Gene regulation in the π-calculus: Simulating cooperativity at the lambda switch
-
Transactions on Computational Systems Biology VII, Springer
-
Kuttler C., and Niehren J. Gene regulation in the π-calculus: Simulating cooperativity at the lambda switch. Transactions on Computational Systems Biology VII. LNCS vol. 4230 (2006), Springer 24-55
-
(2006)
LNCS
, vol.4230
, pp. 24-55
-
-
Kuttler, C.1
Niehren, J.2
-
43
-
-
67650089911
-
-
NuMSV model checker. Available at
-
NuMSV model checker. Available at http://nusmv.irst.itc.it
-
-
-
-
44
-
-
34250895518
-
A simple calculus for proteins and cells
-
Laneve C., and Tarissan F. A simple calculus for proteins and cells. ENTCS vol. 180(3) (2007) 139-154
-
(2007)
ENTCS
, vol.180 3
, pp. 139-154
-
-
Laneve, C.1
Tarissan, F.2
-
45
-
-
33644877164
-
BioModels database: A free centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems
-
Le Novére N., Bornstein B., Broicher A., Courtot M., Donizelli M., Dharuri H., Li L., Sauro H., Schilstra M., Shapiro B., Snoep J.L., and Hucka M. BioModels database: A free centralized database of curated, published, quantitative kinetic models of biochemical and cellular systems. Nucleic Acids Research 34 (2006) D689-D691
-
(2006)
Nucleic Acids Research
, vol.34
-
-
Le Novére, N.1
Bornstein, B.2
Broicher, A.3
Courtot, M.4
Donizelli, M.5
Dharuri, H.6
Li, L.7
Sauro, H.8
Schilstra, M.9
Shapiro, B.10
Snoep, J.L.11
Hucka, M.12
-
46
-
-
26444448026
-
Beta-binders for biological interactions
-
Proc. of CMSB'04, Springer
-
Priami C., and Quaglia P. Beta-binders for biological interactions. Proc. of CMSB'04. LNCS vol. 3082 (2005), Springer 20-33
-
(2005)
LNCS
, vol.3082
, pp. 20-33
-
-
Priami, C.1
Quaglia, P.2
-
47
-
-
0035888407
-
Application of a stochastic name-passing calculus to representation and simulation of molecular processes
-
Priami C., Regev A., Silverman W., and Shapiro E. Application of a stochastic name-passing calculus to representation and simulation of molecular processes. Information Processing Letters 80 (2001) 25-31
-
(2001)
Information Processing Letters
, vol.80
, pp. 25-31
-
-
Priami, C.1
Regev, A.2
Silverman, W.3
Shapiro, E.4
-
48
-
-
0043001070
-
-
Prism web site. http://www.prismmodelchecker.org/
-
Prism web site
-
-
-
49
-
-
67650075489
-
-
BIOSPI Project. Available at
-
BIOSPI Project. Available at http://www.wisdom.weizmann.ac.il/biospi/
-
-
-
-
50
-
-
38049104446
-
-
SPIM, Available at
-
SPIM, The stochastic Pi-Machine. Available at www.doc.ic.ac.uk/anp/spim/
-
The stochastic Pi-Machine
-
-
-
51
-
-
67650097484
-
-
The Kappa Factory. http://www.lix.polytechnique.fr/~krivine/kappaFactory.html
-
The Kappa Factory
-
-
|