메뉴 건너뛰기




Volumn 8130 LNBI, Issue , 2013, Pages 19-32

An approximate execution of rule-based multi-level models

Author keywords

Computational biology; Efficient execution; Multi level modeling; Rule based modeling; Tau leaping

Indexed keywords

COMPUTATIONAL BIOLOGY; EFFICIENT EXECUTION; MULTILEVEL MODEL; RULE-BASED MODELS; TAU-LEAPING;

EID: 84885977008     PISSN: 03029743     EISSN: 16113349     Source Type: Book Series    
DOI: 10.1007/978-3-642-40708-6_3     Document Type: Conference Paper
Times cited : (12)

References (25)
  • 4
    • 84876559742 scopus 로고    scopus 로고
    • Tau Leaping Stochastic Simulation Method in P Systems
    • Hoogeboom, H.J., Pǎun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. Springer, Heidelberg
    • Cazzaniga, P., Pescini, D., Besozzi, D., Mauri, G.: Tau Leaping Stochastic Simulation Method in P Systems. In: Hoogeboom, H.J., Pǎun, G., Rozenberg, G., Salomaa, A. (eds.) WMC 2006. LNCS, vol. 4361, pp. 298-313. Springer, Heidelberg (2006)
    • (2006) LNCS , vol.4361 , pp. 298-313
    • Cazzaniga, P.1    Pescini, D.2    Besozzi, D.3    Mauri, G.4
  • 5
  • 6
    • 80054099633 scopus 로고    scopus 로고
    • Toward a comprehensive language for biological systems
    • Faeder, J.R.: Toward a comprehensive language for biological systems. BMC Systems Biology 9(68) (2011)
    • (2011) BMC Systems Biology , vol.9 , Issue.68
    • Faeder, J.R.1
  • 7
    • 0001144902 scopus 로고    scopus 로고
    • Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels
    • Gibson, M.A., Bruck, J.: Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels. The Journal of Chemical Physics 104(9), 1876-1889 (2000)
    • (2000) The Journal of Chemical Physics , vol.104 , Issue.9 , pp. 1876-1889
    • Gibson, M.A.1    Bruck, J.2
  • 8
    • 33645429016 scopus 로고
    • Exact stochastic simulation of coupled chemical reactions
    • Gillespie, D.T.: Exact stochastic simulation of coupled chemical reactions. The Journal of Physical Chemistry 81(25), 2340-2361 (1977)
    • (1977) The Journal of Physical Chemistry , vol.81 , Issue.25 , pp. 2340-2361
    • Gillespie, D.T.1
  • 9
    • 0035933994 scopus 로고    scopus 로고
    • Approximate accelerated stochastic simulation of chemically reacting system
    • Gillespie, D.T.: Approximate accelerated stochastic simulation of chemically reacting system. The Journal of Chemical Physics 115(4), 1716-1733 (2001)
    • (2001) The Journal of Chemical Physics , vol.115 , Issue.4 , pp. 1716-1733
    • Gillespie, D.T.1
  • 11
    • 33749989765 scopus 로고    scopus 로고
    • A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics
    • Harris, L.A., Clancy, P.: A "partitioned leaping" approach for multiscale modeling of chemical reaction dynamics. The Journal of Chem. Physics 125(14) (2006)
    • (2006) The Journal of Chem. Physics , vol.125 , Issue.14
    • Harris, L.A.1    Clancy, P.2
  • 13
    • 70349966117 scopus 로고    scopus 로고
    • Formalisms for Specifying Markovian Population Models
    • Bournez, O., Potapov, I. (eds.) RP 2009. Springer, Heidelberg
    • Henzinger, T.A., Jobstmann, B., Wolf, V.: Formalisms for Specifying Markovian Population Models. In: Bournez, O., Potapov, I. (eds.) RP 2009. LNCS, vol. 5797, pp. 3-23. Springer, Heidelberg (2009)
    • (2009) LNCS , vol.5797 , pp. 3-23
    • Henzinger, T.A.1    Jobstmann, B.2    Wolf, V.3
  • 15
    • 57049138265 scopus 로고    scopus 로고
    • Large-Scale Design Space Exploration of SSA
    • Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. Springer, Heidelberg
    • Jeschke, M., Ewald, R.: Large-Scale Design Space Exploration of SSA. In: Heiner, M., Uhrmacher, A.M. (eds.) CMSB 2008. LNCS (LNBI), vol. 5307, pp. 211-230. Springer, Heidelberg (2008)
    • (2008) LNCS (LNBI) , vol.5307 , pp. 211-230
    • Jeschke, M.1    Ewald, R.2
  • 16
    • 79951511716 scopus 로고    scopus 로고
    • Exploring the Performance of Spatial Stochastic Simulation Algorithms
    • Jeschke, M., Ewald, R., Uhrmacher, A.M.: Exploring the Performance of Spatial Stochastic Simulation Algorithms. The Journal of Computational Physics 230(7), 2562-2574 (2011)
    • (2011) The Journal of Computational Physics , vol.230 , Issue.7 , pp. 2562-2574
    • Jeschke, M.1    Ewald, R.2    Uhrmacher, A.M.3
  • 19
    • 34548695913 scopus 로고    scopus 로고
    • Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics
    • Marquez-Lago, T.T., Burrage, K.: Binomial tau-leap spatial stochastic simulation algorithm for applications in chemical kinetics. The Journal of Chemical Physics 127(10) (2007)
    • (2007) The Journal of Chemical Physics , vol.127 , Issue.10
    • Marquez-Lago, T.T.1    Burrage, K.2
  • 21
    • 80054062207 scopus 로고    scopus 로고
    • Rule-based multi-level modeling of cell biological systems
    • Maus, C., Rybacki, S., Uhrmacher, A.M.: Rule-based multi-level modeling of cell biological systems. BMC Systems Biology 5(166) (2011)
    • (2011) BMC Systems Biology , vol.5 , Issue.166
    • Maus, C.1    Rybacki, S.2    Uhrmacher, A.M.3
  • 22
    • 84865191067 scopus 로고    scopus 로고
    • Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells
    • Mazemondet, O., John, M., Leye, S., Rolfs, A., Uhrmacher, A.M.: Elucidating the Sources of β-Catenin Dynamics in Human Neural Progenitor Cells. PLoS ONE 7(8), e42792 (2012)
    • (2012) PLoS ONE , vol.7 , Issue.8
    • Mazemondet, O.1    John, M.2    Leye, S.3    Rolfs, A.4    Uhrmacher, A.M.5
  • 23
    • 77951585980 scopus 로고    scopus 로고
    • Streamlined formulation of adaptive explicit-implicit tau-leaping with automatic tau selection
    • Sandmann, W.: Streamlined formulation of adaptive explicit-implicit tau-leaping with automatic tau selection. In: Proc. 41st Winder Simulation Conference (WSC 2009), pp. 1104-1112 (2009)
    • (2009) Proc. 41st Winder Simulation Conference (WSC 2009) , pp. 1104-1112
    • Sandmann, W.1
  • 25
    • 3142543968 scopus 로고    scopus 로고
    • Binomial leap methods for simulating stochastic chemical kinetics
    • Tian, T., Burrage, K.: Binomial leap methods for simulating stochastic chemical kinetics. The Journal of Chemical Physics 121(21), 10356-10364 (2004)
    • (2004) The Journal of Chemical Physics , vol.121 , Issue.21 , pp. 10356-10364
    • Tian, T.1    Burrage, K.2


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.