J. Hillston, Process Algebras for Quantitative Analysis, 20th Annual IEEE Symposium on Logic in Computer Science (LICS' 05), pp.26-29, 2005.
DOI : 10.1109/LICS.2005.35

L. Cardelli, On process rate semantics, Theoretical Computer Science, vol.391, issue.3, pp.190-215, 2008.
DOI : 10.1016/j.tcs.2007.11.012

N. Chabrier-rivier, F. Fages, and S. Soliman, The Biochemical Abstract Machine BIOCHAM, In: Computational Methods in Systems Biology, vol.11, pp.172-191, 2004.
DOI : 10.1007/BF03037227

URL : https://hal.archives-ouvertes.fr/inria-00000814

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

A. Regev and E. Shapiro, Cells as Computation, Nature, vol.419, p.343, 2002.
DOI : 10.1007/3-540-36481-1_1

D. Gilbert, M. Heiner, and S. Lehrack, A Unifying Framework for Modelling and Analysing Biochemical Pathways Using Petri Nets, Computational Methods in Systems Biology, International Conference, pp.200-216, 2007.
DOI : 10.1007/978-3-540-75140-3_14

V. Danos, J. Feret, W. Fontana, R. Harmer, and J. Krivine, Rule-Based Modelling of Cellular Signalling, CONCUR -Concurrency Theory, 18th International Conference, pp.17-41, 2007.
DOI : 10.1007/978-3-540-74407-8_3

URL : https://hal.archives-ouvertes.fr/hal-00164297

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

J. Krivine, R. Milner, and A. Troina, Stochastic Bigraphs, 24th Conference on the Mathematical Foundations of Programming Semantics, pp.73-96, 2008.
DOI : 10.1016/j.entcs.2008.10.006

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

C. Kuttler, C. Lhoussaine, and J. Niehren, A Stochastic Pi Calculus for Concurrent Objects, Second International Conference on Algebraic Biology, pp.232-246, 2007.
DOI : 10.1007/978-3-540-73433-8_17

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

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

C. Priami, A. Regev, E. 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

A. Regev, E. M. Panina, W. Silverman, L. Cardelli, and E. 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. Cardelli, Brane Calculi, Computational Methods in Systems Biology, International Conference CMSB, pp.257-278, 2004.
DOI : 10.1016/S0020-0190(01)00214-9

F. Ciocchetta and J. Hillston, Bio-PEPA: An Extension of the Process Algebra PEPA for Biochemical Networks, Electronic Notes in Theoretical Computer Science, vol.194, issue.3, pp.103-117, 2008.
DOI : 10.1016/j.entcs.2007.12.008

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

M. Carbone and S. Maffeis, On the expressive power of polyadic synchronisation in pi-calculus, Nordic Journal of Computing, vol.10, pp.70-98, 2003.

C. Versari, A Core Calculus for a Comparative Analysis of Bio-inspired Calculi, Programming Languages and Systems, pp.411-425, 2007.
DOI : 10.1007/978-3-540-71316-6_28

C. Priami, Stochastic ?-calculus, Computer Journal, vol.6, pp.578-589, 1995.

C. Kuttler, C. Lhoussaine, and J. Niehren, A Stochastic Pi Calculus for Concurrent Objects, 1st International Workshop on Probabilistic Automata and Logics, 2006.
DOI : 10.1007/978-3-540-73433-8_17

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

A. Phillips and L. Cardelli, A correct abstract machine for the stochastic pi-calculus, Proceedings of BioConcur '04, 2004.

C. Versari and N. Busi, Stochastic Simulation of Biological Systems with Dynamical Compartment Structure, Computational Methods in Systems Biology, International Conference, pp.80-95, 2007.
DOI : 10.1007/978-3-540-75140-3_6

J. Jaffar and J. L. Lassez, Constraint logic programming, Proceedings of the 14th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '87, pp.111-119, 1987.
DOI : 10.1145/41625.41635

V. A. Saraswat and M. C. Rinard, Concurrent constraint programming, Proceedings of the 17th ACM SIGPLAN-SIGACT symposium on Principles of programming languages , POPL '90, pp.232-245, 1990.
DOI : 10.1145/96709.96733

M. John, C. Lhoussaine, J. Niehren, and A. Uhrmacher, The Attributed Pi Calculus, 6th International Conference, pp.83-102, 2008.
DOI : 10.1007/978-3-540-88562-7_10

URL : https://hal.archives-ouvertes.fr/inria-00308970

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

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

C. Kuttler, Modeling Bacterial Gene Expression in a Stochastic Pi Calculus with Concurrent Objects, 2007.
URL : https://hal.archives-ouvertes.fr/tel-00111653

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

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

M. Baldamus, J. Parrow, and B. Victor, A Fully Abstract Encoding of the ??-Calculus with Data Terms, Automata, Languages and Programming, 32nd International- Colloquium, pp.1202-1213, 2005.
DOI : 10.1007/11523468_97

M. Johansson, J. Parrow, B. Victor, and J. Bengtson, Extended pi-Calculi, Automata, Languages and Programming, 35th International Colloquium, pp.87-98, 2008.
DOI : 10.1007/978-3-540-70583-3_8

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

C. Priami, P. Quaglia, and A. Romanel, BlenX Static and Dynamic Semantics, Concurrency Theory, 20th International Conference, pp.37-52, 2009.
DOI : 10.1007/11423348_10

M. Maurin, M. Magnin, and O. H. Roux, Modeling of Genetic Regulatory Network in Stochastic ??-Calculus, First International Conference, pp.282-294, 2009.
DOI : 10.1021/j100540a008

P. Lecca, Stochastic pi-calculus models of the molecular bases of parkinson's disease, International Conference on Bioinformatics and Computational Biology, pp.298-304, 2008.

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

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

C. Kuttler, C. Lhoussaine, and M. Nebut, Rule-based modeling of transcriptional attenuation at the tryptophan operon, Transactions on Computational Systems Biology, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00445565

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

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

M. John, R. Ewald, and A. M. Uhrmacher, A Spatial Extension to the Pi Calculus, ENTCS, vol.194, pp.133-148, 2008.
URL : https://hal.archives-ouvertes.fr/hal-00656206

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

M. John, C. Lhoussaine, and J. Niehren, Dynamic Compartments in the Imperative ??-Calculus, 7th International Conference, pp.235-250, 2009.
DOI : 10.1007/978-3-540-71316-6_28

URL : https://hal.archives-ouvertes.fr/inria-00422970

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

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

URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.219.6371

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. 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

R. Pozo and B. Miller, SciMark 2.0, 2009.

D. Degenring, M. Roehl, and A. 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

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, Proceedings of the Winter Simulation Conference, 2009.
URL : https://hal.archives-ouvertes.fr/hal-00656195

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