메뉴 건너뛰기




Volumn , Issue , 2012, Pages 447-453

Modelling biological pathway dynamics with Timed Automata

Author keywords

dynamic behaviour; modelling; signalling pathway; timed automata

Indexed keywords

BIOLOGICAL CELLS; BIOLOGICAL INTERACTIONS; BIOLOGICAL NETWORKS; BIOLOGICAL PATHWAYS; CELL BEHAVIOURS; COMPLEX INTERACTION; DISCRETIZATIONS; DOMAIN SPECIFIC LANGUAGES; DYNAMIC BEHAVIOURS; EVENT MODEL; EXECUTABLE MODEL; EXPRESSIVE POWER; FORMAL SEMANTICS; GROWTH FACTOR; SIGNALLING MOLECULES; SIGNALLING NETWORK; SIGNALLING PATHWAYS; TIMED AUTOMATA; UPPAAL MODEL CHECKERS; USER FRIENDLY INTERFACE;

EID: 84872875140     PISSN: None     EISSN: None     Source Type: Conference Proceeding    
DOI: 10.1109/BIBE.2012.6399719     Document Type: Conference Paper
Times cited : (12)

References (17)
  • 1
    • 36049044199 scopus 로고    scopus 로고
    • Executable cell biology
    • Nov.
    • J. Fisher and T. A. Henzinger, "Executable cell biology." Nature biotechnology, vol. 25, no. 11, pp. 1239-1249, Nov. 2007.
    • (2007) Nature Biotechnology , vol.25 , Issue.11 , pp. 1239-1249
    • Fisher, J.1    Henzinger, T.A.2
  • 2
    • 65649138437 scopus 로고    scopus 로고
    • Computational modeling of biochemical networks using COPASI systems biology
    • ser. I. V. Maly, J. M. Walker, and J. M. Walker, Eds. Totowa, NJ: Humana Press, ch. 2
    • P. Mendes, S. Hoops, S. Sahle, R. Gauges, J. Dada, and U. Kummer, "Computational modeling of biochemical networks using COPASI systems biology," ser. Methods in Molecular Biology, I. V. Maly, J. M. Walker, and J. M. Walker, Eds. Totowa, NJ: Humana Press, 2009, vol. 500, ch. 2, pp. 17-59.
    • (2009) Methods in Molecular Biology , vol.500 , pp. 17-59
    • Mendes, P.1    Hoops, S.2    Sahle, S.3    Gauges, R.4    Dada, J.5    Kummer, U.6
  • 3
    • 0345269975 scopus 로고    scopus 로고
    • Genetic Network Analyzer: Qualitative simulation of genetic regulatory networks
    • Feb.
    • H. de Jong, J. Geiselmann, C. Hernandez, and M. Page, "Genetic Network Analyzer: qualitative simulation of genetic regulatory networks," Bioinformatics, vol. 19, no. 3, pp. 336-344, Feb. 2003.
    • (2003) Bioinformatics , vol.19 , Issue.3 , pp. 336-344
    • De Jong, H.1    Geiselmann, J.2    Hernandez, C.3    Page, M.4
  • 5
    • 57049132896 scopus 로고    scopus 로고
    • Modelling and simulation of biological processes in BlenX
    • March
    • L. Dematté, C. Priami, and A. Romanel, "Modelling and simulation of biological processes in BlenX," SIGMETRICS Perform. Eval. Rev., vol. 35, pp. 32-39, March 2008.
    • (2008) SIGMETRICS Perform. Eval. Rev. , vol.35 , pp. 32-39
    • Dematté, L.1    Priami, C.2    Romanel, A.3
  • 6
    • 65549101937 scopus 로고    scopus 로고
    • Bio-PEPA: A framework for the modelling and analysis of biological systems
    • August
    • F. Ciocchetta and J. Hillston, "Bio-PEPA: A framework for the modelling and analysis of biological systems," Theor. Comput. Sci., vol. 410, pp. 3065-3084, August 2009.
    • (2009) Theor. Comput. Sci. , vol.410 , pp. 3065-3084
    • Ciocchetta, F.1    Hillston, J.2
  • 7
    • 77950314677 scopus 로고    scopus 로고
    • Modelling and analysis of the NF-κB pathway in Bio-PEPA
    • Transactions on Computational Systems Biology XII, ser. C. Priami, R. Breitling, D. Gilbert, M. Heiner, and A. Uhrmacher, Eds. Springer Berlin / Heidelberg
    • F. Ciocchetta, A. Degasperi, J. Heath, and J. Hillston, "Modelling and analysis of the NF-κB pathway in Bio-PEPA," in Transactions on Computational Systems Biology XII, ser. Lecture Notes in Computer Science, C. Priami, R. Breitling, D. Gilbert, M. Heiner, and A. Uhrmacher, Eds. Springer Berlin / Heidelberg, 2010, vol. 5945, pp. 229-262.
    • (2010) Lecture Notes in Computer Science , vol.5945 , pp. 229-262
    • Ciocchetta, F.1    Degasperi, A.2    Heath, J.3    Hillston, J.4
  • 8
    • 79960371032 scopus 로고    scopus 로고
    • BlenX models of α-synuclein and parkin kinetics in neuropathology of Parkinson's disease
    • June
    • P. Lecca, "BlenX models of α-synuclein and parkin kinetics in neuropathology of Parkinson's disease," Journal of Biological Systems, vol. 19, pp. 149-181, June 2011.
    • (2011) Journal of Biological Systems , vol.19 , pp. 149-181
    • Lecca, P.1
  • 9
    • 0028413052 scopus 로고
    • A theory of timed automata
    • April
    • R. Alur and D. L. Dill, "A theory of timed automata," Theor. Comput. Sci., vol. 126, pp. 183-235, April 1994.
    • (1994) Theor. Comput. Sci. , vol.126 , pp. 183-235
    • Alur, R.1    Dill, D.L.2
  • 10
    • 84872858742 scopus 로고    scopus 로고
    • ANIMO, http://wwwhome.ewi.utwente.nl/~schivos/animo.
    • ANIMO
  • 11
    • 70349581497 scopus 로고    scopus 로고
    • Cytoscape: A community-based framework for network modeling
    • Clifton, N.J.
    • S. Killcoyne, G. W. Carter, J. Smith, and J. Boyle, "Cytoscape: a community-based framework for network modeling." Methods in molecular biology (Clifton, N.J.), vol. 563, pp. 219-239, 2009.
    • (2009) Methods in Molecular Biology , vol.563 , pp. 219-239
    • Killcoyne, S.1    Carter, G.W.2    Smith, J.3    Boyle, J.4
  • 13
    • 84949215100 scopus 로고    scopus 로고
    • Model checking
    • Foundations of Software Technology and Theoretical Computer Science, ser. S. Ramesh and G. Sivakumar, Eds. Springer Berlin / Heidelberg
    • E. Clarke, "Model checking," in Foundations of Software Technology and Theoretical Computer Science, ser. Lecture Notes in Computer Science, S. Ramesh and G. Sivakumar, Eds. Springer Berlin / Heidelberg, 1997, vol. 1346, pp. 54-56.
    • (1997) Lecture Notes in Computer Science , vol.1346 , pp. 54-56
    • Clarke, E.1
  • 14
    • 47149087560 scopus 로고    scopus 로고
    • Approximating continuous systems by timed automata
    • Formal Methods in Systems Biology, ser. J. Fisher, Ed. Springer Berlin / Heidelberg
    • O. Maler and G. Batt, "Approximating continuous systems by timed automata," in Formal Methods in Systems Biology, ser. Lecture Notes in Computer Science, J. Fisher, Ed. Springer Berlin / Heidelberg, 2008, vol. 5054, pp. 77-89.
    • (2008) Lecture Notes in Computer Science , vol.5054 , pp. 77-89
    • Maler, O.1    Batt, G.2
  • 15
    • 33847355217 scopus 로고    scopus 로고
    • Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate
    • Feb.
    • S. D. M. Santos, P. J. Verveer, and P. I. H. Bastiaens, "Growth factor-induced MAPK network topology shapes Erk response determining PC-12 cell fate," Nature Cell Biology, vol. 9, no. 3, pp. 324-330, Feb. 2007.
    • (2007) Nature Cell Biology , vol.9 , Issue.3 , pp. 324-330
    • Santos, S.D.M.1    Verveer, P.J.2    Bastiaens, P.I.H.3
  • 16
    • 79960376940 scopus 로고    scopus 로고
    • Time for statistical model checking of real-time systems
    • Computer Aided Verification, ser. G. Gopalakrishnan and S. Qadeer, Eds. Springer Berlin / Heidelberg
    • A. David, K. Larsen, A. Legay, M. Mikučionis, and Z. Wang, "Time for statistical model checking of real-time systems," in Computer Aided Verification, ser. Lecture Notes in Computer Science, G. Gopalakrishnan and S. Qadeer, Eds. Springer Berlin / Heidelberg, 2011, vol. 6806, pp. 349-355.
    • (2011) Lecture Notes in Computer Science , vol.6806 , pp. 349-355
    • David, A.1    Larsen, K.2    Legay, A.3    Mikučionis, M.4    Wang, Z.5
  • 17
    • 79959216670 scopus 로고    scopus 로고
    • Model-based testing and some steps towards test-based modelling
    • Formal Methods for Eternal Networked Software Systems, ser. M. Bernardo and V. Issarny, Eds. Springer Berlin / Heidelberg
    • J. Tretmans, "Model-based testing and some steps towards test-based modelling," in Formal Methods for Eternal Networked Software Systems, ser. Lecture Notes in Computer Science, M. Bernardo and V. Issarny, Eds. Springer Berlin / Heidelberg, 2011, vol. 6659, pp. 297-326.
    • (2011) Lecture Notes in Computer Science , vol.6659 , pp. 297-326
    • Tretmans, J.1


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.