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Tytuł artykułu

A Calculus of Looping Sequences for Modelling Microbiological Systems

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Języki publikacji
EN
Abstrakty
EN
The paper presents the Calculus of Looping Sequences (CLS) suitable to describe microbiological systems and their evolution. The terms of the calculus are constructed by basic constituent elements and operators of sequencing, looping, containment and parallel composition. The looping operator allows tying up the ends of a sequence, thus creating a circular sequence which can represent a membrane. We show that a membrane calculus recently proposed can be encoded into CLS. We use our calculus to model interactions among bacteria and bacteriophage viruses, and to reason on their properties.
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Wydawca
Rocznik
Strony
21--35
Opis fizyczny
bibliogr. 14 poz.
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autor
autor
Bibliografia
  • [1] R. Alur, C. Belta, F. Ivancic, V. Kumar, M. Mintz, G.J. Pappas, H. Rubin and J. Schug. "Hybrid modeling and simulation of biomolecular networks". In Hybrid Systems: Computation and Control, LNCS 2034, pages 19-32, Springer, 2001.
  • [2] R. Barbuti, S. Cataudella, A. Maggiolo-Schettini, P. Milazzo and A. Troina. "A probabilistic model for molecular systems". Fundamenta Informaticae, volume 67, pages 13-27, 2005.
  • [3] R. Barbuti, A. Maggiolo-Schettini, P. Milazzo and A. Troina. "An alternative to Gillespie's algorithm for simulating chemical reactions". Computational Methods in Systems Biology (CMSB'05), Edinburgh, 2005.
  • [4] L. Cardelli. "Bioware languages". In Computer Systems. Theory, Technology and Applications. Papers for Roger Needham, Springer, pages 59-66, 2003.
  • [5] L. Cardelli. "Brane calculi. interactions of biological membranes". Computational Methods in Systems Biology (CMSB'04), LNCS 3082, pages 257-280, Springer, 2005.
  • [6] N. Chabrier-Rivier, M. Chiaverini, V. Danos, F. Fages and V. Schachter. "Modeling and querying biomolecular interaction networks". Theoretical Computer Science, volume 325, number 1, pages 25-44, 2004.
  • [7] M. Curti, P. Degano, C. Priami and C.T. Baldari. "Modelling biochemical pathways through enhanced pi-calculus". Theoretical Computer Science, volume 325, number 1, pages 111-140, 2004.
  • [8] V. Danos and C. Laneve. "Formal molecular biology". Theoretical Computer Science, volume 325, number 1, pages 69-110, 2004.
  • [9] C. Flanagan and M. Abadi. "Object types against races". CONCUR'99, LNCS 1664, pages 288-303, Springer, 1999.
  • [10] A. Gordon and P. Hankin. "A concurrent object calculus: reduction and typing". High-Level Concurrent Languages (HLCL'98), Elsevier ENTCS, volume 16, number 3, 1998.
  • [11] H. Matsuno, A. Doi, M. Nagasaki and S. Miyano."Hybrid Petri net representation of gene regulatory network". In Pacific Symposium on Biocomputing,World Scientific Press, pages 341-352, 2000.
  • [12] G. Pǎun. "Membrane computing. an introduction". Springer, 2002.
  • [13] A. Regev, E.M. Panina, W. Silverman, L. Cardelli and E. Shapiro. "BioAmbients: an abstraction for biological compartments". Theoretical Computer Science, volume 325, number 1, pages 141-167, 2004.
  • [14] A. Regev,W. Silverman and E.Y. Shapiro. "Representation and simulation of biochemical processes using the pi-calculus process algebra". Pacific Symposium on Biocomputing,World Scientific Press, pages 459-470, 2001.
Typ dokumentu
Bibliografia
Identyfikator YADDA
bwmeta1.element.baztech-article-BUS2-0010-0051
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