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.
Mots-clés : system biology, predictive modelling, CLS, type systems
@article{ITA_2011__45_1_35_0, 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/} }
TY - JOUR AU - Bioglio, Livio TI - Enumerated type semantics for the calculus of looping sequences JO - RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications PY - 2011 SP - 35 EP - 58 VL - 45 IS - 1 PB - EDP-Sciences UR - http://archive.numdam.org/articles/10.1051/ita/2011010/ DO - 10.1051/ita/2011010 LA - en ID - ITA_2011__45_1_35_0 ER -
%0 Journal Article %A Bioglio, Livio %T Enumerated type semantics for the calculus of looping sequences %J RAIRO - Theoretical Informatics and Applications - Informatique Théorique et Applications %D 2011 %P 35-58 %V 45 %N 1 %I EDP-Sciences %U http://archive.numdam.org/articles/10.1051/ita/2011010/ %R 10.1051/ita/2011010 %G en %F ITA_2011__45_1_35_0
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] Hybrid modeling and simulation of biomolecular networks, in Hybrid Systems: Computation and Control. Lecture Notes in Computer Science 2034 (2001) 19-32. | Zbl
, , and ,[2] 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.
, and ,[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] 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
, , and ,[5] A calculus of looping sequences for modelling microbiological systems. Fund. Inform. 72 (2006) 21-35. | MR | Zbl
, , and ,[6] Type directed semantics for the calculus of looping sequences. International Journal of Software and Informatics (2010), to appear.
, , and ,[7] Brane calculi - interactions of biological membranes, in Computational Methods in Systems Biology (2004) 257-278. | Zbl
,[8] Formal molecular biology. Theoret. Comput. Sci. 325 (2004) 69-110. | MR | Zbl
and ,[9] 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.
, and ,[10] 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.
, , and ,[11] Qualitative and Quantitative Formal Modeling of Biological Systems. Ph.D. thesis, University of Pisa (2007).
,[12] Membrane Computing. An Introduction. Springer-Verlag (2002). | MR | Zbl
,[13] Cells as computation. Nature 419 (2002) 343.
and ,[14] The -calculus as an abstraction for biomolecular systems. Modelling in Molecular Biology (2004) 219-266. | MR
and ,[15] Bioambients: An abstraction for biological compartments. Theoret. Comput. Sci. 325 (2004) 141-167. | MR | Zbl
, , , and ,[16] Mathematics of multisets, in Multiset Processing. Lecture Notes in Computer Science 2235 (2001) 347-358. | MR | Zbl
,[17] 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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