M. Abadi and C. Fournet, Mobile values, new names, and secure communication, POPL, pp.104-115, 2001.
DOI : 10.1145/373243.360213

URL : https://hal.archives-ouvertes.fr/hal-01423924

. Hybrid-automata, An algorithmic approach to the specification and verification of hybrid systems, Hybrid Systems, pp.209-229

H. Anai, K. Horimoto, and T. Kutsia, Algebraic Biology, Second International Conference Proceedings, volume 4545 of Lecture Notes in Computer Science, 2007.
DOI : 10.1007/978-3-540-73433-8

M. Baldamus, J. Parrow, and B. Victor, A fully abstract encoding of the pi-calculus with data terms, Lecture Notes in Computer Science, vol.3580, pp.244-1202, 2005.

R. Barbuti, G. Caravagna, A. Maggiolo-schettini, P. Milazzo, and G. Pardini, The Calculus of Looping Sequences, SFM, pp.387-423, 2008.
DOI : 10.1007/978-3-540-68894-5_11

R. Barbuti, A. Maggiolo-schettini, P. Milazzo, and G. Pardini, Spatial Calculus of Looping Sequences, Electronic Notes in Theoretical Computer Science, vol.229, issue.1, pp.21-39, 2009.
DOI : 10.1016/j.entcs.2009.02.003

H. P. Barendregt, The Lambda Calculus, Its Syntax and Semantics (Studies in Logic and the Foundations of Mathematics, 1985.

E. Bartocci, F. Corradini, M. R. Berardini, E. Merelli, and L. Tesei, Shape calculus: A spatial calculus for 3d colliding shapes, 2009.

L. Bortolussi and A. Policriti, Hybrid Semantics for Stochastic ??-Calculus, Lecture Notes in Computer Science, vol.5147, pp.40-55, 2008.
DOI : 10.1007/978-3-540-85101-1_4

L. Bortolussi and A. Policriti, Modeling Biological Systems in Stochastic Concurrent Constraint Programming, Constraints, vol.99, issue.9, pp.66-90, 2008.
DOI : 10.1007/s10601-007-9034-8

H. Bowman and R. Gomez, Concurrency Theory: Calculi an Automata for Modelling Untimed and Timed Concurrent Systems, 2005.

L. Brodo, P. Degano, and C. Priami, A Stochastic Semantics for BioAmbients, PaCT, pp.22-34, 2007.
DOI : 10.1007/978-3-540-73940-1_3

M. Calder and S. Gilmore, Computational Methods in Systems Biology, International Conference Proceedings, volume 4695 of Lecture Notes in Computer Science, 2007.
DOI : 10.1007/978-3-540-75140-3

L. Calzone, F. Fages, and S. Soliman, BIOCHAM: an environment for modeling biological systems and formalizing experimental knowledge, Bioinformatics, vol.22, issue.14, pp.221805-1807, 2006.
DOI : 10.1093/bioinformatics/btl172

URL : https://hal.archives-ouvertes.fr/hal-01431364

I. Cappello and P. Quaglia, A Translation of Beta-binders in a Prioritized Pi-calculus, Electronic Notes in Theoretical Computer Science, vol.229, issue.1, pp.109-125, 2009.
DOI : 10.1016/j.entcs.2009.02.008

L. Cardelli, Brane Calculi, Lecture Notes in Computer Science, vol.80, issue.2, pp.257-278, 2004.
DOI : 10.1016/S0020-0190(01)00214-9

L. Cardelli, E. Caron, P. Gardner, O. Kahramanogullari, and A. Phillips, A process model of Rho GTP-binding proteins, Theoretical Computer Science, vol.410, issue.33-34, pp.33-343166, 2009.
DOI : 10.1016/j.tcs.2009.04.029

L. Cardelli and P. Gardner, Processes in space, 2009.

C. Chaouiya, Petri net modelling of biological networks, Briefings in Bioinformatics, vol.8, issue.4, pp.29-30, 2007.
DOI : 10.1093/bib/bbm029

N. A. Chebotareva, B. I. Kurganov, and N. B. Livanova, Biochemical effects of molecular crowding, Biochemistry (Moscow), vol.274, issue.11, pp.691239-1251, 2004.
DOI : 10.1007/s10541-005-0070-y

A. Church, A formulation of the simple theory of types, The Journal of Symbolic Logic, vol.1, issue.02, pp.56-68, 1940.
DOI : 10.2307/2371199

F. Ciocchetta and M. L. Guerriero, Modelling Biological Compartments in Bio-PEPA, Electronic Notes in Theoretical Computer Science, vol.227, pp.77-95, 2009.
DOI : 10.1016/j.entcs.2008.12.105

F. Ciocchetta and J. Hillston, Bio-PEPA: A framework for the modelling and analysis of biological systems, Theoretical Computer Science, vol.410, issue.33-34, pp.33-343065, 2009.
DOI : 10.1016/j.tcs.2009.02.037

W. Damm and D. Harel, Lscs: Breathing life into message sequence charts, Formal Methods in System Design, vol.19, issue.1, pp.45-80, 2001.
DOI : 10.1023/A:1011227529550

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.20.5472

V. Danos and C. Laneve, Formal molecular biology, Theoretical Computer Science, vol.325, issue.1, pp.69-110, 2004.
DOI : 10.1016/j.tcs.2004.03.065

URL : https://hal.archives-ouvertes.fr/hal-00164591

D. Degenring, M. Röhl, and A. M. Uhrmacher, Discrete event, multi-level simulation of metabolite channeling, Biosystems, vol.75, issue.1-3, pp.29-41, 2004.
DOI : 10.1016/j.biosystems.2004.03.008

L. Dematté, C. Priami, and A. Romanel, The Beta Workbench: a computational tool to study the dynamics of biological systems, Briefings in Bioinformatics, vol.9, issue.5, pp.437-449, 2008.
DOI : 10.1093/bib/bbn023

L. Dematté, C. Priami, and A. Romanel, Modelling and simulation of biological processes in BlenX, ACM SIGMETRICS Performance Evaluation Review, vol.35, issue.4, pp.32-39, 2008.
DOI : 10.1145/1364644.1364653

A. Deutsch and S. Dormann, Cellular Automaton Modeling of Biological Pattern Formation, Birkhäuser Boston, 2004.

C. Ene and T. Muntean, Expressiveness of point-to-point versus broadcast communications, Lecture Notes in Computer Science, vol.1684, pp.258-268, 1999.
DOI : 10.1007/3-540-48321-7_21

T. Engelmann, Ueber Licht- und Farbenperception niederster Organismen, Pfl??ger, Archiv f??r die Gesammte Physiologie des Menschen und der Thiere, vol.29, issue.1, pp.387-400, 1882.
DOI : 10.1007/BF01612047

J. R. Faeder, M. L. Blinov, B. Goldstein, and W. S. Hlavacek, Rule-based modeling of biochemical networks, Complexity, vol.1, issue.4, pp.22-41, 2005.
DOI : 10.1002/cplx.20074

F. Fages and A. Rizk, On the Analysis of Numerical Data Time Series in Temporal Logic, pp.48-63, 2007.
DOI : 10.1007/978-3-540-75140-3_4

F. Fages and S. Soliman, Abstract interpretation and types for systems biology, Theoretical Computer Science, vol.403, issue.1, pp.52-70, 2008.
DOI : 10.1016/j.tcs.2008.04.024

URL : https://hal.archives-ouvertes.fr/hal-01431355

J. Fisher, N. Piterman, . Hubbard, M. J. Stern, and D. Harel, Computational insights into Caenorhabditis elegans vulval development, Proceedings of the National Academy of Sciences, vol.102, issue.6, pp.1951-1956, 2005.
DOI : 10.1073/pnas.0409433102

URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC548551

M. A. Gibson and J. Bruck, Efficient Exact Stochastic Simulation of Chemical Systems with Many Species and Many Channels, The Journal of Physical Chemistry A, vol.104, issue.9, pp.1876-1889, 2000.
DOI : 10.1021/jp993732q

D. T. Gillespie, A general method for numerically simulating the stochastic time evolution of coupled chemical reactions, Journal of Computational Physics, vol.22, issue.4, pp.403-434, 1976.
DOI : 10.1016/0021-9991(76)90041-3

D. T. Gillespie, Exact stochastic simulation of coupled chemical reactions, The Journal of Physical Chemistry, vol.81, issue.25, pp.2340-2361, 1977.
DOI : 10.1021/j100540a008

M. L. Guerriero, C. Priami, and A. Romanel, Modeling Static Biological Compartments with Beta-binders, In Anai et al, pp.247-261, 2007.
DOI : 10.1007/978-3-540-73433-8_18

F. Haack, S. Leye, and A. M. Uhrmacher, A flexible architecture for modeling and simulation of diffusional association, Electronic Proceedings in Theoretical Computer Science, vol.19, pp.70-84, 1002.
DOI : 10.4204/EPTCS.19.5

S. Hardy and P. Robillard, MODELING AND SIMULATION OF MOLECULAR BIOLOGY SYSTEMS USING PETRI NETS: MODELING GOALS OF VARIOUS APPROACHES, Journal of Bioinformatics and Computational Biology, vol.02, issue.04, pp.595-613, 2004.
DOI : 10.1142/S0219720004000764

D. Harel, Statecharts: a visual formalism for complex systems, Science of Computer Programming, vol.8, issue.3, pp.231-274, 1987.
DOI : 10.1016/0167-6423(87)90035-9

L. A. Harris, J. S. Hogg, and F. , Compartmental rule-based modeling of biochemical systems, Proceedings of the 2009 Winter Simulation Conference (WSC), 2009.
DOI : 10.1109/WSC.2009.5429719

M. Heiner and A. M. Uhrmacher, Computational Methods in Systems Biology, 6th International Conference Proceedings, volume 5307 of Lecture Notes in Computer Science, 2008.
DOI : 10.1007/978-3-540-88562-7

J. Himmelspach and A. M. Uhrmacher, Plug'n Simulate, 40th Annual Simulation Symposium (ANSS'07), pp.137-143, 2007.
DOI : 10.1109/ANSS.2007.34

G. P. Huet, Confluent Reductions: Abstract Properties and Applications to Term Rewriting Systems: Abstract Properties and Applications to Term Rewriting Systems, Journal of the ACM, vol.27, issue.4, pp.797-821, 1980.
DOI : 10.1145/322217.322230

M. Jeschke, A. M. Uhrmacher, S. J. Mason, R. R. Hill, L. Mönch et al., Multi-resolution spatial simulation for molecular crowding, 2008 Winter Simulation Conference, pp.1384-1392, 2008.
DOI : 10.1109/WSC.2008.4736214

M. Johansson, J. Parrow, B. Victor, and J. Bengtson, Extended pi-Calculi, Lecture Notes in Computer Science, vol.5126, issue.2, pp.87-98, 2008.
DOI : 10.1007/978-3-540-70583-3_8

M. John, R. Ewald, and A. M. Uhrmacher, A Spatial Extension to the ?? Calculus, Electronic Notes in Theoretical Computer Science, vol.194, issue.3, pp.133-148, 2008.
DOI : 10.1016/j.entcs.2007.12.010

URL : https://hal.archives-ouvertes.fr/hal-00656206

N. Kam, H. Kugler, R. Marelly, L. Appleby, J. Fisher et al., A scenario-based approach to modeling development: A prototype model of C. elegans vulval fate specification, Developmental Biology, vol.323, issue.1, p.1, 2008.
DOI : 10.1016/j.ydbio.2008.07.030

B. N. Kholodenko, Cell-signalling dynamics in time and space, Nature Reviews Molecular Cell Biology, vol.20, issue.3, pp.165-176, 2006.
DOI : 10.1038/nrm1838

V. Khomenko and R. Meyer, Checking pi-Calculus Structural Congruence is Graph Isomorphism Complete, 2009 Ninth International Conference on Application of Concurrency to System Design, 2008.
DOI : 10.1109/ACSD.2009.8

L. B. Kier, Modeling Chemical Systems Using Cellular Automata, 2005.

H. Kitano, Computational systems biology, Nature, vol.14, issue.6912, pp.206-210, 2002.
DOI : 10.1038/35002125

H. Kitano, Systems Biology: A Brief Overview, Science, vol.295, issue.5560, pp.1662-1664, 2002.
DOI : 10.1126/science.1069492

E. Klipp, W. Liebermeister, C. Wierling, A. Kowald, H. Lehrach et al., Systems Biology: A Textbook, 2009.

E. Krieghoff, J. Behrens, and B. Mayr, Nucleo-cytoplasmic distribution of ??-catenin is regulated by retention, Journal of Cell Science, vol.119, issue.7, pp.1453-1463, 2006.
DOI : 10.1242/jcs.02864

J. Krivine, R. Milner, and A. Troina, Stochastic Bigraphs, Electronic Notes in Theoretical Computer Science, vol.218, pp.73-96, 2008.
DOI : 10.1016/j.entcs.2008.10.006

URL : https://hal.archives-ouvertes.fr/hal-00530712

C. Kuttler, Modeling Bacterial Gene Expression in a Stochastic Pi-Calculus with Concurrent Objects, 2006.
URL : https://hal.archives-ouvertes.fr/tel-00111653

C. Kuttler, C. Lhoussaine, and M. Nebut, Rule-based modeling of transcriptional attenuation at the tryptophan operon, Transactions on Computaional Systems Biology XII. Special Issue on Modeling Methodologies LNCS (Lecture Notes in Bioinformatics), vol.5945, pp.199-228, 2010.
URL : https://hal.archives-ouvertes.fr/hal-00445565

C. Kuttler, C. Lhoussaine, and J. And-niehren, A Stochastic Pi Calculus for Concurrent Objects, In Anai et al, pp.232-246, 2007.
DOI : 10.1007/978-3-540-73433-8_17

URL : https://hal.archives-ouvertes.fr/inria-00121104

C. Kuttler and J. Niehren, Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch, Transactions on Computational Systems Biology, vol.4230, pp.24-55, 2006.
DOI : 10.1007/11905455_2

URL : https://hal.archives-ouvertes.fr/inria-00089218

M. Z. Kwiatkowska, G. Norman, P. , and D. , PRISM 2.0: a tool for probabilistic model checking, First International Conference on the Quantitative Evaluation of Systems, 2004. QEST 2004. Proceedings., pp.322-323, 2004.
DOI : 10.1109/QEST.2004.1348048

M. Kwiatkowski and I. Stark, The continuous pi-calculus: A process algebra for biochemical modelling, Heiner and Uhrmacher, pp.103-122, 2008.

G. F. Lawler, Introduction to Stochastic Processes., Chapman & Hall/CRC Probability Series). Chapman and Hall/CRC, 2006.
DOI : 10.2307/2533988

S. Leye, M. John, and A. M. Uhrmacher, A flexible architecture for performance experiments with the pi-Calculus and its extensions, Proceedings of the 3rd International ICST Conference on Simulation Tools and Techniques, 2010.
DOI : 10.4108/ICST.SIMUTOOLS2010.8820

M. Matsumoto and T. Nishimura, Mersenne twister: a 623-dimensionally equidistributed uniform pseudo-random number generator, ACM Transactions on Modeling and Computer Simulation, vol.8, issue.1, pp.3-30, 1998.
DOI : 10.1145/272991.272995

C. Maus, Component-Based Modelling of RNA Structure Folding, pp.44-62, 2008.
DOI : 10.1007/978-3-540-88562-7_8

O. Mazemondet, M. John, C. Maus, A. M. Uhrmacher, and A. Rolfs, Integrating diverse reaction types into stochastic models -a signaling pathway case study in the imperative pi-calculus, pp.932-943, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00656195

H. H. Mcadams and A. Arkin, It???s a noisy business! Genetic regulation at the nanomolar scale, Trends in Genetics, vol.15, issue.2, pp.65-69, 1999.
DOI : 10.1016/S0168-9525(98)01659-X

E. Merino and C. Yanofsky, Transcription attenuation: a highly conserved regulatory strategy used by bacteria, Trends in Genetics, vol.21, issue.5, pp.260-264, 2005.
DOI : 10.1016/j.tig.2005.03.002

T. Millat, E. Bullinger, J. Rohwer, and O. Wolkenhauer, Approximations and their consequences for dynamic modelling of signal transduction pathways, Mathematical Biosciences, vol.207, issue.1, pp.40-57, 2007.
DOI : 10.1016/j.mbs.2006.08.012

R. Milner, Communicating and Mobile Systems: The Pi Calculus, 1999.

R. Milner, The Space and Motion of Communicating Agents, 2009.
DOI : 10.1017/CBO9780511626661

R. Milner, J. Parrow, and D. Walker, A calculus of mobile processes, i. Information and Computation, pp.1-40, 1992.

G. Mirams, H. Byrne, and J. King, A multiple timescale analysis of a mathematical model of the Wnt/??-catenin signalling pathway, Journal of Mathematical Biology, vol.581, issue.1, pp.131-160, 2010.
DOI : 10.1007/s00285-009-0262-y

J. C. Mitchell, Foundations for Programming Languages, 1996.

I. Mura, D. Prandi, C. Priami, and A. Romanel, Exploiting non-Markovian Bio-Processes, Electronic Notes in Theoretical Computer Science, vol.253, issue.3, pp.83-98, 2009.
DOI : 10.1016/j.entcs.2009.10.007

URL : http://doi.org/10.1016/j.entcs.2009.10.007

M. Nagao, M. Sugimori, and M. Nakafuku, Cross Talk between Notch and Growth Factor/Cytokine Signaling Pathways in Neural Stem Cells, Molecular and Cellular Biology, vol.27, issue.11, pp.273982-3994, 2007.
DOI : 10.1128/MCB.00170-07

J. Niehren, Uniform confluence in concurrent computation, Journal of Functional Programming, vol.10, issue.5, pp.453-499, 2000.
DOI : 10.1017/S0956796800003762

URL : https://hal.archives-ouvertes.fr/inria-00536801

C. Palamidessi, Comparing the expressive power of the synchronous and asynchronous $pi$ -calculi, Mathematical Structures in Computer Science, vol.13, issue.5, pp.685-719, 2003.
DOI : 10.1017/S0960129503004043

URL : https://hal.archives-ouvertes.fr/inria-00201104

G. Paun, Computing with Membranes, Journal of Computer and System Sciences, vol.61, issue.1, pp.108-143, 2000.
DOI : 10.1006/jcss.1999.1693

M. Pedersen and G. Plotkin, A Language for Biochemical Systems: Design and Formal Specification, Transactions on Computational Systems Biology XII, vol.25, issue.18, pp.77-145, 2010.
DOI : 10.1093/bioinformatics/btp401

C. A. Petri, Kommunikatin mit Automaten, 1962.

A. Phillips and L. Cardelli, Efficient, Correct Simulation of Biological Processes in the Stochastic Pi-calculus, pp.184-199, 2007.
DOI : 10.1007/978-3-540-75140-3_13

B. C. Pierce, Types and Programming Languages, 2002.

T. D. Pollard, The cytoskeleton, cellular motility and the reductionist agenda, Nature, vol.29, issue.6933, pp.741-745, 2003.
DOI : 10.1038/nature01598

C. Priami, Stochastic ??-Calculus, The Computer Journal, vol.38, issue.7, pp.578-589, 1995.
DOI : 10.1093/comjnl/38.7.578

C. Priami, A. Regev, E. Y. Shapiro, and W. Silverman, Application of a stochastic name-passing calculus to representation and simulation of molecular processes, Information Processing Letters, vol.80, issue.1, pp.25-31, 2001.
DOI : 10.1016/S0020-0190(01)00214-9

M. Ptashne and A. Gann, Genes and Signals, 2001.

A. Ralston, Simultaneous gene transcription and translation in bacteria, Nature Education, vol.1, issue.1, 2008.

A. Regev, Computational Systems Biology: A Calculus for Biomolecular Knowledge, 2003.

A. Regev, E. M. Panina, W. Silverman, L. Cardelli, and E. Y. Shapiro, BioAmbients: an abstraction for biological compartments, Theoretical Computer Science, vol.325, issue.1, pp.141-167, 2004.
DOI : 10.1016/j.tcs.2004.03.061

L. E. Reichl, A Modern Course in Statistical Physics (Physics Textbook), 2009.

A. Saarinen, M. Linne, and O. Yli-harja, Stochastic differential equation model for cerebellar granule cell excitability, 2008.

O. Schaeffer, On the Use of Process Algebra Techniques in Computational Modeling of Cancer Initiation and Development, 2008.

A. Schäfer and M. John, Conceptional modeling and analysis of spatio-temporal processes in biomolecular systems, APCCM, volume 96 of CRPIT, pp.39-48, 2009.

W. W. Tait, Intensional interpretations of functionals of finite type I, The Journal of Symbolic Logic, vol.91, issue.02, pp.198-212, 1967.
DOI : 10.1007/BF01447860

K. Takahashi, S. Nanda, V. Arjunan, and M. Tomita, Space in systems biology of signaling pathways - towards intracellular molecular crowding in silico, FEBS Letters, vol.20, issue.8, pp.5791783-1788, 2005.
DOI : 10.1016/j.febslet.2005.01.072

A. M. Uhrmacher, Dynamic structures in modeling and simulation: a reflective approach, ACM Transactions on Modeling and Computer Simulation, vol.11, issue.2, pp.206-232, 2001.
DOI : 10.1145/384169.384173

A. M. Uhrmacher, R. Ewald, M. John, C. Maus, M. Jeschke et al., Combining micro and macro-modeling in DEVS for computational biology, 2007 Winter Simulation Conference, pp.871-880, 2007.
DOI : 10.1109/WSC.2007.4419683

C. Versari, A Core Calculus for a Comparative Analysis of Bio-inspired Calculi, Lecture Notes in Computer Science, vol.4421, pp.411-425, 2007.
DOI : 10.1007/978-3-540-71316-6_28

C. Versari, Encoding Catalytic P Systems in ??@, Electronic Notes in Theoretical Computer Science, vol.171, issue.2, pp.171-186, 2007.
DOI : 10.1016/j.entcs.2007.05.015

C. Versari, A Core Calculus for the Analysis and Implementation of Biologically Inspired Languages, 2009.

C. Versari and N. Busi, Stochastic biological modelling in the presence of multiple compartments, Theoretical Computer Science, vol.410, issue.33-34, pp.33-343039, 2009.
DOI : 10.1016/j.tcs.2009.03.038

C. Versari, N. Busi, and R. Gorrieri, An expressiveness study of priority in process calculi, Mathematical Structures in Computer Science, vol.4703, issue.06, pp.1161-1189, 2009.
DOI : 10.1016/0890-5401(92)90008-4

C. Wawra, M. Kühl, and H. A. Kestler, Extended analyses of the Wnt/??-catenin pathway: Robustness and oscillatory behaviour, FEBS Letters, vol.65, issue.21, pp.5814043-4048, 2007.
DOI : 10.1016/j.febslet.2007.07.043

B. P. Zeigler, H. Praehofer, K. , and T. G. , Theory of Modeling and Simulation, Second Edition, 2000.