메뉴 건너뛰기




Volumn 111, Issue 2-3, 2013, Pages 129-136

Modelling, abstraction, and computation in systems biology: A view from computer science

Author keywords

Abstraction; Algorithmic biological modelling; Biological computation; Multi scale modelling

Indexed keywords

ARTICLE; BIOLOGICAL MODEL; COMPUTER SIMULATION; INTERDISCIPLINARY EDUCATION; METHODOLOGY; SYSTEMS BIOLOGY;

EID: 84878156120     PISSN: 00796107     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.pbiomolbio.2012.08.015     Document Type: Article
Times cited : (16)

References (72)
  • 2
    • 62149131337 scopus 로고    scopus 로고
    • Compartmentalized signalling: spatial regulation of camp by the action of compartmentalized phosphodiesterases
    • February
    • Baillie George S. Compartmentalized signalling: spatial regulation of camp by the action of compartmentalized phosphodiesterases. FEBS Journal February 2009, 726(7):1790-1799.
    • (2009) FEBS Journal , vol.726 , Issue.7 , pp. 1790-1799
    • Baillie, G.S.1
  • 3
    • 0036969667 scopus 로고    scopus 로고
    • BioComplexity: a pluralist research strategy is necessary for a mechanistic explanation of the " live" state
    • Bruggeman F.J., Westerhoff H.V., Boogerd F.C. BioComplexity: a pluralist research strategy is necessary for a mechanistic explanation of the " live" state. Philosophical Psychology 2002, 15(4):411-440.
    • (2002) Philosophical Psychology , vol.15 , Issue.4 , pp. 411-440
    • Bruggeman, F.J.1    Westerhoff, H.V.2    Boogerd, F.C.3
  • 4
    • 70450185589 scopus 로고    scopus 로고
    • Process algebra modelling styles for biomolecular processes
    • Springer-Verlag, C. Priami, R.-J. Back, I. Petre (Eds.) Transactions on Computational Systems Biology XI
    • Calder Muffy, Hillston Jane Process algebra modelling styles for biomolecular processes. Lecture Notes in Bioinformatics 2009, vol. 5750:1-25. Springer-Verlag. C. Priami, R.-J. Back, I. Petre (Eds.).
    • (2009) Lecture Notes in Bioinformatics , vol.5750 , pp. 1-25
    • Calder, M.1    Hillston, J.2
  • 5
    • 33845385005 scopus 로고    scopus 로고
    • Analysis of signalling pathways using continuous time markov chains
    • Springer-Verlag, C. Priami, G. Plotkin (Eds.) Transactions on Computational Systems Biology VI
    • Calder Muffy, Vyshemirsky Vladislav, Gilbert David, Orton Richard Analysis of signalling pathways using continuous time markov chains. Lecture Notes in Bioinformatics 2006, vol. 4220:44-67. Springer-Verlag. C. Priami, G. Plotkin (Eds.).
    • (2006) Lecture Notes in Bioinformatics , vol.4220 , pp. 44-67
    • Calder, M.1    Vyshemirsky, V.2    Gilbert, D.3    Orton, R.4
  • 6
    • 84878146950 scopus 로고
    • An algebraic approach to hardware description and verification. PhD thesis, University of Edinburgh, Department of Computer Science, April
    • Luca Cardelli., An algebraic approach to hardware description and verification. PhD thesis, University of Edinburgh, Department of Computer Science, April 1982.
    • (1982)
    • Cardelli, L.1
  • 7
    • 33745647409 scopus 로고    scopus 로고
    • Brane Calculi
    • Springer-Verlag, V. Danos, V. Schächter (Eds.) Computational Methods in Systems Biology, International Conference, CMSB 2004, Paris, France, May 26-28, 2004, Revised Selected Papers
    • Cardelli Luca Brane Calculi. Lecture Notes in Computer Science 2004, vol. 3082:257-278. Springer-Verlag. V. Danos, V. Schächter (Eds.).
    • (2004) Lecture Notes in Computer Science , vol.3082 , pp. 257-278
    • Cardelli, L.1
  • 8
    • 33845196533 scopus 로고    scopus 로고
    • Abstract machines of systems biology
    • Springer Verlag, C. Priami, E. Merelli (Eds.) Gonzalez, Pedro Pablo, and Omicini, Andrea, Editors, Transactions on Computational Systems Biology III
    • Cardelli Luca Abstract machines of systems biology. Lecture Notes in Computer Science 2005, vol. 3737:145-168. Springer Verlag. C. Priami, E. Merelli (Eds.).
    • (2005) Lecture Notes in Computer Science , vol.3737 , pp. 145-168
    • Cardelli, L.1
  • 11
    • 45749134288 scopus 로고    scopus 로고
    • Process algebras in systems biology
    • Springer, M. Bernardo, P. Degano, G. Zavattaro (Eds.) Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008, Bertinoro, Italy, June 2-7, 2008, Advanced Lectures
    • Ciocchetta Federica, Hillston Jane Process algebras in systems biology. Lecture Notes in Computer Science 2008, vol. 5016:265-312. Springer. M. Bernardo, P. Degano, G. Zavattaro (Eds.).
    • (2008) Lecture Notes in Computer Science , vol.5016 , pp. 265-312
    • Ciocchetta, F.1    Hillston, J.2
  • 12
    • 0000078696 scopus 로고    scopus 로고
    • Stratgic directions in concurrency research
    • December
    • Cleaveland Rance, Smolka Scott A., et al. Stratgic directions in concurrency research. ACM Computing Surveys December 1996, 28(4).
    • (1996) ACM Computing Surveys , vol.28 , Issue.4
    • Cleaveland, R.1    Smolka, S.A.2
  • 13
    • 34047105227 scopus 로고    scopus 로고
    • Explaining a complex living system: dynamics, multi-scaling, and emergence
    • Cohen Irun R., Harel David Explaining a complex living system: dynamics, multi-scaling, and emergence. Journal of the Royal Society Interface 2007, 4:175-182.
    • (2007) Journal of the Royal Society Interface , vol.4 , pp. 175-182
    • Cohen, I.R.1    Harel, D.2
  • 14
    • 79251538979 scopus 로고    scopus 로고
    • Proving stabilization of biological systems
    • Springer-Verlag, Proceedings of the 12th International Conference on Verification, Model Checking, and Abstract Interpretation
    • Cook Byron, Fisher Jasmin, Krepska Elzbieta, Piterman Nir Proving stabilization of biological systems. Lecture Notes in Computer Science 2011, vol. 6538:134-149. Springer-Verlag.
    • (2011) Lecture Notes in Computer Science , vol.6538 , pp. 134-149
    • Cook, B.1    Fisher, J.2    Krepska, E.3    Piterman, N.4
  • 15
    • 38149083357 scopus 로고    scopus 로고
    • Rule-based modelling of cellular signalling
    • Springer-Verlag, L. Caires, V.T. Vasconcelos (Eds.) CONCUR 2007-Concurrency Theory; 18th International Conference, CONCUR 2007; Proceedings
    • Danos Vincent, Feret Jérôme, Fontana Walter, Harmer Russell, Krivine Jean Rule-based modelling of cellular signalling. Lecture Notes in Computer Science 2007, vol. 4703:17-41. Springer-Verlag. L. Caires, V.T. Vasconcelos (Eds.).
    • (2007) Lecture Notes in Computer Science , vol.4703 , pp. 17-41
    • Danos, V.1    Feret Jérôme2    Fontana, W.3    Harmer, R.4    Krivine, J.5
  • 18
    • 79960906495 scopus 로고    scopus 로고
    • A sat-based algorithm for computing attractors in synchronous boolean networks
    • September/October
    • Dubrova Elena, Teslenko Maxim A sat-based algorithm for computing attractors in synchronous boolean networks. IEEE/ACM Transactions on Computational Biology and Bioinformatics September/October 2011, 8(5):1393-1399.
    • (2011) IEEE/ACM Transactions on Computational Biology and Bioinformatics , vol.8 , Issue.5 , pp. 1393-1399
    • Dubrova, E.1    Teslenko, M.2
  • 20
    • 17844384842 scopus 로고    scopus 로고
    • Reactive animation: realistic modeling of complex dynamic systems
    • Efroni Sol, Harel David, Cohen Irun R. Reactive animation: realistic modeling of complex dynamic systems. IEEE Computer 2005, 38(1):38-47.
    • (2005) IEEE Computer , vol.38 , Issue.1 , pp. 38-47
    • Efroni, S.1    Harel, D.2    Cohen, I.R.3
  • 21
    • 0022514018 scopus 로고
    • " sometimes" and " not never" revisted: on branching versus linear time temporal logic
    • January
    • Emerson E.Allen, Halpern Joseph Y. " sometimes" and " not never" revisted: on branching versus linear time temporal logic. Journal of the Association for Computing Machinery January 1986, 33(I):151-178.
    • (1986) Journal of the Association for Computing Machinery , vol.33 , Issue.I , pp. 151-178
    • Emerson, E.A.1    Halpern, J.Y.2
  • 23
    • 84878163972 scopus 로고    scopus 로고
    • Proceedings of the 1st International Workshop on Static Analysis and Systems Biology (SASB 2010), 1st International Workshop on Static Analysis and Systems Biology
    • May J. Feret, A. Levchenko (Eds.)
    • Proceedings of the 1st International Workshop on Static Analysis and Systems Biology (SASB 2010), 1st International Workshop on Static Analysis and Systems Biology. Electronic Notes in Theoretical Computer Science May 2011, vol. 272. J. Feret, A. Levchenko (Eds.).
    • (2011) Electronic Notes in Theoretical Computer Science , vol.272
  • 24
    • 36049044199 scopus 로고    scopus 로고
    • Executable cell biology
    • November
    • Fisher Jasmin, Henzinger Thomas A. Executable cell biology. Nature Biotechnology November 2007, 25(11):1239-1249.
    • (2007) Nature Biotechnology , vol.25 , Issue.11 , pp. 1239-1249
    • Fisher, J.1    Henzinger, T.A.2
  • 25
    • 77950347868 scopus 로고    scopus 로고
    • The executable pathway to biological networks
    • Fisher Jasmin, Piterman Nor The executable pathway to biological networks. Briefings in Functional Genomics 2010, 9(1):79-92.
    • (2010) Briefings in Functional Genomics , vol.9 , Issue.1 , pp. 79-92
    • Fisher, J.1    Piterman, N.2
  • 27
    • 38749110325 scopus 로고    scopus 로고
    • Levelism and the Method of Abstraction
    • IEG Research Report 22.11.04, Information Ethics Group: Oxford University, University of Bari
    • Floridi, Luciano, Sanders, J.W. Levelism and the Method of Abstraction. IEG Research Report 22.11.04, Information Ethics Group: Oxford University, University of Bari, 2004.
    • (2004)
    • Floridi1    Luciano2    Sanders, J.W.3
  • 29
    • 0015609281 scopus 로고
    • The logical analysis of continuous, non-linear biochemical control networks
    • Glass Leon, Kaufmann Stuart A. The logical analysis of continuous, non-linear biochemical control networks. Journal of Theoretical Biology 1973, 39(1):103-129.
    • (1973) Journal of Theoretical Biology , vol.39 , Issue.1 , pp. 103-129
    • Glass, L.1    Kaufmann, S.A.2
  • 32
    • 46149089691 scopus 로고    scopus 로고
    • Comprehensive and realistic modeling of biological systems
    • L.F. Perrone, F.P. Wieland, J. Liu, B.G. Lawson, D.M. Nicol, R.M. Fujimoto (Eds.)
    • Harel David Comprehensive and realistic modeling of biological systems. Proceedings of the 2006 Winter Simulation Conference 2006, 1625-1627. L.F. Perrone, F.P. Wieland, J. Liu, B.G. Lawson, D.M. Nicol, R.M. Fujimoto (Eds.).
    • (2006) Proceedings of the 2006 Winter Simulation Conference , pp. 1625-1627
    • Harel, D.1
  • 33
    • 77950398306 scopus 로고    scopus 로고
    • Life is complicated
    • April
    • Hayden Erika Check Life is complicated. Nature April 2010, 464:664-667.
    • (2010) Nature , vol.464 , pp. 664-667
    • Hayden, E.C.1
  • 34
  • 35
    • 84958609259 scopus 로고    scopus 로고
    • Model validation of biological pathways using petri nets - demonstrated for apoptosis
    • Springer-Verlag, C. Priami (Ed.) Computational Methods in Systems Biology; First International Workshop, CMSB 2003; Proceedings
    • Heiner Monika, Koch Ina, Will Jürgen Model validation of biological pathways using petri nets - demonstrated for apoptosis. Lecture Notes in Computer Science 2003, vol. 2602:173. Springer-Verlag. C. Priami (Ed.).
    • (2003) Lecture Notes in Computer Science , vol.2602 , pp. 173
    • Heiner, M.1    Koch, I.2    Will Jürgen3
  • 36
    • 45749112203 scopus 로고    scopus 로고
    • Petri nets for systems and synthetic biology
    • Springer, M. Bernardo, P. Degano, G. Zavattaro (Eds.) Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008, Bertinoro, Italy, June 2-7, 2008, Advanced Lectures
    • Heiner Monika, Gilbert David, Donaldson Robin Petri nets for systems and synthetic biology. Lecture Notes in Computer Science 2008, vol. 5016:215-264. Springer. M. Bernardo, P. Degano, G. Zavattaro (Eds.).
    • (2008) Lecture Notes in Computer Science , vol.5016 , pp. 215-264
    • Heiner, M.1    Gilbert, D.2    Donaldson, R.3
  • 39
    • 0000118661 scopus 로고
    • Abstract interpretation: a semantics-based tool for program analysis
    • Oxford University Press
    • Jones Neil, Nielson Flemming Abstract interpretation: a semantics-based tool for program analysis. In Handbook of Logic in Computer Science 1994, vol. 4. Oxford University Press.
    • (1994) In Handbook of Logic in Computer Science , vol.4
    • Jones, N.1    Nielson, F.2
  • 43
    • 77954510016 scopus 로고    scopus 로고
    • Biocharts: a visual formalism for complex biological systems
    • July
    • Kugler Hillel, Larjo Antti, Harel David Biocharts: a visual formalism for complex biological systems. Journal of the Royal Society Interface July 2010, 7(48):1015-1024.
    • (2010) Journal of the Royal Society Interface , vol.7 , Issue.48 , pp. 1015-1024
    • Kugler, H.1    Larjo, A.2    Harel, D.3
  • 44
    • 0002897966 scopus 로고
    • Metaphor in science
    • Cambridge University Press, A. Ortony (Ed.)
    • Kuhn Thomas Metaphor in science. Metaphor and Thought 1979, 409-419. Cambridge University Press. A. Ortony (Ed.).
    • (1979) Metaphor and Thought , pp. 409-419
    • Kuhn, T.1
  • 46
    • 84864937829 scopus 로고    scopus 로고
    • Probabilistic model checking for systems biology
    • Jones and Bartlett, M. Sriram Iyengar (Ed.)
    • Kwiatkowska Marta, Norman Gethin, Parker David Probabilistic model checking for systems biology. Symbolic Systems Biology 2010, 31-59. Jones and Bartlett. M. Sriram Iyengar (Ed.).
    • (2010) Symbolic Systems Biology , pp. 31-59
    • Kwiatkowska, M.1    Norman, G.2    Parker, D.3
  • 48
    • 84878151372 scopus 로고    scopus 로고
    • Searching for a Conceptual Language in Systems Biology: Hints from statistical mechanics?
    • Matek Christian Searching for a Conceptual Language in Systems Biology: Hints from statistical mechanics?. Progress in Biophysics and Molecular Biology 2013, 111(2-3):116-118.
    • (2013) Progress in Biophysics and Molecular Biology , vol.111 , Issue.2-3 , pp. 116-118
    • Matek, C.1
  • 49
    • 0005667380 scopus 로고
    • Higher Order Logic and Hardware Verification
    • Cambridge University Press
    • Melham T. Higher Order Logic and Hardware Verification. Cambridge Tracts in Theoretical Computer Science 1993, vol. 31. Cambridge University Press.
    • (1993) Cambridge Tracts in Theoretical Computer Science , vol.31
    • Melham, T.1
  • 54
    • 37349057040 scopus 로고    scopus 로고
    • Claude Bernard, the first systems biologist, and the future of physiology
    • Noble Denis Claude Bernard, the first systems biologist, and the future of physiology. Experimental Physiology 2008, 91(1):16-26.
    • (2008) Experimental Physiology , vol.91 , Issue.1 , pp. 16-26
    • Noble, D.1
  • 55
    • 84878120232 scopus 로고    scopus 로고
    • A Biological Relativity View of the Relationships Between Genomes and Phenotypes
    • Noble Denis A Biological Relativity View of the Relationships Between Genomes and Phenotypes. Progress in Biophysics and Molecular Biology 2013, 111(2-3):59-65.
    • (2013) Progress in Biophysics and Molecular Biology , vol.111 , Issue.2-3 , pp. 59-65
    • Noble, D.1
  • 56
    • 84878163484 scopus 로고    scopus 로고
    • A programming language for composable dna circuits
    • June
    • Phillips Andrew, Cardelli Luca A programming language for composable dna circuits. Journal of the Royal Society Interface June 2009, 7(48):1015-1024.
    • (2009) Journal of the Royal Society Interface , vol.7 , Issue.48 , pp. 1015-1024
    • Phillips, A.1    Cardelli, L.2
  • 57
    • 38549129227 scopus 로고    scopus 로고
    • Computational thinking in biology
    • Springer-Verlag, C. Priami (Ed.)
    • Priami Corrado Computational thinking in biology. Transactions on Computational Systems Biology VIII 2007, 63-76. Springer-Verlag. C. Priami (Ed.).
    • (2007) Transactions on Computational Systems Biology VIII , pp. 63-76
    • Priami, C.1
  • 58
    • 67049143968 scopus 로고    scopus 로고
    • Algorithmic systems biology
    • May
    • Priami Corrado Algorithmic systems biology. Communications of the ACM May 2009, 52(5):80-88.
    • (2009) Communications of the ACM , vol.52 , Issue.5 , pp. 80-88
    • Priami, C.1
  • 61
    • 34948874342 scopus 로고    scopus 로고
    • Qualitative networks: a symbolic approach to analyze biological signaling networks
    • Schaub Marc A., Henzinger Thomas A., Fisher Jasmin Qualitative networks: a symbolic approach to analyze biological signaling networks. BMC Systems Biology 2007, 1.
    • (2007) BMC Systems Biology , vol.1
    • Schaub, M.A.1    Henzinger, T.A.2    Fisher, J.3
  • 63
    • 45849151727 scopus 로고    scopus 로고
    • Pathway logic
    • Springer, M. Bernardo, P. Degano, G. Zavattaro (Eds.) Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2008, Bertinoro, Italy, June 2-7, 2008, Advanced Lectures
    • Talcott Carolyn L. Pathway logic. Lecture Notes in Computer Science 2008, vol. 5016:21-53. Springer. M. Bernardo, P. Degano, G. Zavattaro (Eds.).
    • (2008) Lecture Notes in Computer Science , vol.5016 , pp. 21-53
    • Talcott, C.L.1
  • 65
    • 84960561455 scopus 로고
    • On computable numbers, with an application to the entscheidungs problem
    • Turing A.M. On computable numbers, with an application to the entscheidungs problem. Proceedings of the London Mathematical Society 1937, 42(2):230-265.
    • (1937) Proceedings of the London Mathematical Society , vol.42 , Issue.2 , pp. 230-265
    • Turing, A.M.1
  • 66
    • 37049235151 scopus 로고
    • The theory of open systems in physics and biology
    • January
    • von Bertalanffy Ludwig The theory of open systems in physics and biology. Science January 1950, 111:23-29.
    • (1950) Science , vol.111 , pp. 23-29
    • von Bertalanffy, L.1
  • 67
    • 0034877874 scopus 로고    scopus 로고
    • The silicon cell, not dead but alive!
    • Westerhoff Hans V. The silicon cell, not dead but alive!. Metabolic Engineering 2001, 3:207-210.
    • (2001) Metabolic Engineering , vol.3 , pp. 207-210
    • Westerhoff, H.V.1
  • 69
    • 51849116469 scopus 로고    scopus 로고
    • Computational thinking and thinking about computing
    • July
    • Wing Jeannette M. Computational thinking and thinking about computing. Philosophical Transactions of the Royal Society A July 2008, 366:3717-3725.
    • (2008) Philosophical Transactions of the Royal Society A , vol.366 , pp. 3717-3725
    • Wing, J.M.1
  • 70
    • 0342397274 scopus 로고
    • A compositional model of MOS circuits
    • Kluwer Academic Publishers, G.M. Birtwistle, P.A. Subrahmanyam (Eds.)
    • Winskel Glynn A compositional model of MOS circuits. VLSI Specification, Verification and Synthesis 1987, 323-347. Kluwer Academic Publishers. G.M. Birtwistle, P.A. Subrahmanyam (Eds.).
    • (1987) VLSI Specification, Verification and Synthesis , pp. 323-347
    • Winskel, G.1
  • 71


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.