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Biological transactions for quantitative models. (English) Zbl 1277.68173
Busi, Nadia (ed.) et al., Proceedings of the first workshop on membrane computing and biologically inspired process calculi (MeCBIC 2006), S. Servolo, Venice, Italy, July 9, 2006. Amsterdam: Elsevier. Electronic Notes in Theoretical Computer Science 171, No. 2, 55-67 (2007).
Summary: In this work an extension of stochastic \(\pi\)-calculus with biological transactions is presented. This permits to model multi-reactant multi-product reactions as atomic actions when quantitative information are given. First, the syntax and the semantics are defined, then some transaction properties are discussed. Finally, some examples are described.
For the entire collection see [Zbl 1273.68017].

MSC:
68Q85 Models and methods for concurrent and distributed computing (process algebras, bisimulation, transition nets, etc.)
68Q55 Semantics in the theory of computing
92C42 Systems biology, networks
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[1] Bistarelli, S.; Cervesato, I.; Lenzini, G.; Marangoni, R.; Martinelli, F., On representing biological systems through multiset rewriting, ()
[2] Bistarelli, S.; Cervesato, I.; Lenzini, G.; Martinelli, F., Relating multiset rewriting and process algebras for security protocol analysis, Journal of computer security, 13, (2005)
[3] Blossey, R., C. Kuttler and J. Niehren, Gene regulation in the π-calculus: simulating cooperativity at the lambda switch, Proc. of BioConcur 2004, 2004.
[4] Butler, M.; Hoare, T.; Ferreira, C., A trace semantics for long-running transactions, (), 133-150 · Zbl 1081.68644
[5] Bocchi, L.; Laneve, C.; Zavattaro, G., A calculus for long-running transactions, () · Zbl 1253.68056
[6] Busi, N.; Zavattaro, G., On the serializability of transactions in javaspaces, ()
[7] Cardelli, L.; Panina, E.M.; Regev, A.; Shapiro, E.; Silverman, W., Bioambients: an abstraction for biological compartments, Theoretical computer science, 235, 141-167, (2004), Elsevier · Zbl 1069.68569
[8] Cho, K.H.; Kolch, W.; Ullah, M.; Wolkenhauer, O., Modelling and simulation of intracellular dynamics: choosing an appropriate framework, IEEE transactions on nanobioscience, 3, 200-207, (2004)
[9] Ciocchetta, F. and C. Priami, “The stochastic π-calculus with biological transactions”, Technical Report \bfTR-02-2006, The Microsoft Research-University of Trento Centre for Computational and Systems Biology, 2006. · Zbl 1277.68173
[10] Costantin, G.; Laudanna, C.; Lecca, P.; Priami, C.; Quaglia, P.; 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, 273-288, (2003)
[11] Danos, V. and J. Krivine, Formal molecular biology done in CCS-R, Proc. of Workshop on Concurrent Models in MolecularBiology (BioConcur ’03), 2003.
[12] Danos, V.; Laneve, C., Core formal molecular biology, (), 302-318 · Zbl 1033.92013
[13] Gillespie, D.T., Exact stochastic simulation of coupled chemical reactions, Journal of physical chemistry, 81, 2340-2361, (1977)
[14] Kitano, H., Systems biology: A brief overview, Science, 295, 1662-1664, (2002)
[15] Laneve, C.; Zavattaro, G., Foundations of web transactions, (), 282-298 · Zbl 1118.68335
[16] Milner, R., Communicating and mobile systems: the π-calculus, (1999), Cambridge University Press · Zbl 0942.68002
[17] Priami, C.; Regev, A.; Silverman, W.; Shapiro, E., Application of a stochastic name-passing calculus to representation and simulation of molecular processes, Information processing letters, 80, 25-31, (2001) · Zbl 0997.92018
[18] Priami, C. and P. Quaglia, Beta-binders for biological interactions, Proc. of Computational Methods in Systems Biology ’04 (CMSB04), 2004. · Zbl 1088.68646
[19] Regev, A., Representation and simulation of molecular pathways in the stochastic π-calculus, Proc. of the 2nd workshop on Computation of Biochemical Pathways and Genetic Networks, 2001.
[20] Sangiorgi, D.; Walker, D., The π-calculus: a theory of mobile processes, (2001), Cambridge University Press · Zbl 0981.68116
[21] Tyson, J., Some further studies of nonlinear oscillators in chemical systems, J. chem. phys., 58, 3919-3930, (1973)
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