no. 1
Enumerated type semantics for the calculus of looping sequences
RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 45 (2011) no. 1, pp. 35-58.

The calculus of looping sequences is a formalism for describing the evolution of biological systems by means of term rewriting rules. In this paper we enrich this calculus with a type discipline which preserves some biological properties depending on the minimum and the maximum number of elements of some type requested by the present elements. The type system enforces these properties and typed reductions guarantee that evolution preserves them. As an example, we model the hemoglobin structure and the equilibrium between cell death and division: typed reductions prevent undesirable behaviors.

DOI : 10.1051/ita/2011010
Classification : 03B15, 68Q42, 68Q55, 68Q65, 92C42
Mots clés : system biology, predictive modelling, CLS, type systems 
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     author = {Bioglio, Livio},
     title = {Enumerated type semantics for the calculus of looping sequences},
     journal = {RAIRO - Theoretical Informatics and Applications - Informatique Th\'eorique et Applications},
     pages = {35--58},
     publisher = {EDP-Sciences},
     volume = {45},
     number = {1},
     year = {2011},
     doi = {10.1051/ita/2011010},
     mrnumber = {2776853},
     zbl = {1214.92028},
     language = {en},
     url = {http://archive.numdam.org/articles/10.1051/ita/2011010/}
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Bioglio, Livio. Enumerated type semantics for the calculus of looping sequences. RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications, Tome 45 (2011) no. 1, pp. 35-58. doi : 10.1051/ita/2011010. http://archive.numdam.org/articles/10.1051/ita/2011010/

[1] R. Alur, C. Belta, V. Kumar and M. Mintz, Hybrid modeling and simulation of biomolecular networks, in Hybrid Systems: Computation and Control. Lecture Notes in Computer Science 2034 (2001) 19-32. | Zbl

[2] B. Aman, M. Dezani-Ciancaglini and A. Troina, Type Disciplines for Analysing Biologically Relevant Properties, in Membrane Computing and Biologically Inspired Process Calculi (MeCBIC'08). Electronic Notes in Theoretical Computer Science 227 (2009) 97-111.

[3] R. Barbuti, A. Maggiolo-schettini and P. Milazzo, Extending the calculus of looping sequences to model protein interaction at the domain level, in Proceedings of International Symposium on Bioinformatics Research and Applications (ISBRA'07). Lecture Notes in Bioinformatics 4463 (2006) 638-649.

[4] R. Barbuti, A. Maggiolo-Schettini, P. Milazzo and A. Troina, Bisimulation congruences in the calculus of looping sequences, in Proceedings of International Colloquium on Theoretical Aspects of Computing (ICTAC'06). Lecture Notes in Computer Science 4281 (2006) 93-107. | MR | Zbl

[5] R. Barbuti, A. Maggiolo-Schettini, P. Milazzo and A. Troina, A calculus of looping sequences for modelling microbiological systems. Fund. Inform. 72 (2006) 21-35. | MR | Zbl

[6] L. Bioglio, M. Dezani-Ciancaglini, P. Giannini and A. Troina, Type directed semantics for the calculus of looping sequences. International Journal of Software and Informatics (2010), to appear.

[7] L. Cardelli, Brane calculi - interactions of biological membranes, in Computational Methods in Systems Biology (2004) 257-278. | Zbl

[8] V. Danos and C. Laneve, Formal molecular biology. Theoret. Comput. Sci. 325 (2004) 69-110. | MR | Zbl

[9] M. Dezani-Ciancaglini, P. Giannini and A. Troina, A Type System for Required/Excluded Elements in CLS, in Workshop on Developments in Computational Models (DCM'09). Electronic Proceedings in Theoretical Computer Science 9 (2009) 38-48.

[10] H. Matsuno, A. Doi, M. Nagasaki and S. Miyano, Hybrid Petri Net representation of gene regulatory networks, in Proceedings of the Pacific Symposium on Biocomputing (PSB '00) (2000), 338-349. http://www.marmisicc.com/index.aspx?IDMenu=76&idMenuAPP=11.

[11] P. Milazzo, Qualitative and Quantitative Formal Modeling of Biological Systems. Ph.D. thesis, University of Pisa (2007).

[12] G. Păun, Membrane Computing. An Introduction. Springer-Verlag (2002). | MR | Zbl

[13] A. Regev and E. Shapiro, Cells as computation. Nature 419 (2002) 343.

[14] A. Regev and E. Shapiro, The π-calculus as an abstraction for biomolecular systems. Modelling in Molecular Biology (2004) 219-266. | MR

[15] A. Regev, E.M. Panina, W. Silverman, L. Cardelli and E. Shapiro, Bioambients: An abstraction for biological compartments. Theoret. Comput. Sci. 325 (2004) 141-167. | MR | Zbl

[16] A. Syropoulos, Mathematics of multisets, in Multiset Processing. Lecture Notes in Computer Science 2235 (2001) 347-358. | MR | Zbl

[17] J.B. Wells, The essence of principal typings, in Proceedings of Intenational Colloquium on Automata, Languages and Programming (ICALP'02). Lecture Notes in Computer Science 2380 (2002) 913-925. | MR | Zbl

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