D. Angeli, P. De-leenheer, and E. D. Sontag, A Petri Net Approach to Persistence Analysis in Chemical Reaction Networks, Biology and Control Theory: Current Challenges, pp.181-216, 2007.
DOI : 10.1007/978-3-540-71988-5_9

M. Ashburner, C. A. Ball, J. A. Blake, D. Botstein, H. Butler et al., Gene Ontology: tool for the unification of biology, Nature Genetics, vol.9, issue.1, pp.25-29, 2000.
DOI : 10.1038/75556

A. Ballesta, S. Dulong, C. Abbara, B. Cohen, A. Okyar et al., A combined experimental and mathematical approach for molecularbased optimization of irinotecan circadian delivery, PLOS Computational Biology, vol.7, issue.9, 2011.
URL : https://hal.archives-ouvertes.fr/inserm-00692053

J. Banâtre and D. L. Métayer, Chemical Reaction as a Computational Model, Functional Programmming, pp.103-117, 1989.
DOI : 10.1007/978-1-4471-3166-3_7

J. Banâtre and T. Priol, Chemical programming of future serviceoriented architectures, Jounral of Software, vol.4, pp.738-746, 2009.

G. Bernot, J. Comet, A. Richard, and J. Guespin, Application of formal methods to biological regulatory networks: extending Thomas??? asynchronous logical approach with temporal logic, Journal of Theoretical Biology, vol.229, issue.3, pp.339-347, 2004.
DOI : 10.1016/j.jtbi.2004.04.003

G. Berry and G. Boudol, The chemical abstract machine, Theoretical Computer Science, vol.96, 1992.
URL : https://hal.archives-ouvertes.fr/inria-00075426

L. Cardelli, Brane calculi -interactions of biological membranes, Proceedings of the second international workshop on Computational Methods in Systems Biology, pp.257-280, 2004.

N. Chabrier-rivier, M. Chiaverini, and V. Danos, Modeling and querying biomolecular interaction networks, Theoretical Computer Science, vol.325, issue.1, pp.25-44, 2004.
DOI : 10.1016/j.tcs.2004.03.063

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

V. Chelliah, C. Laibe, and N. Novère, BioModels Database: A Repository of Mathematical Models of Biological Processes, Silico Systems Biology, pp.189-199, 2013.
DOI : 10.1007/978-1-62703-450-0_10

A. Cimatti, E. Clarke, F. G. , E. Giunchiglia, M. Pistore et al., NuSMV 2: An OpenSource Tool for Symbolic Model Checking, Proceedings of the International Conference on Computer-Aided Verification, CAV'02, 2002.
DOI : 10.1007/3-540-45657-0_29

E. M. Clarke, Orna Grumberg, and Doron A. Peled. Model Checking, 1999.

P. Cousot and R. Cousot, Abstract interpretation, Proceedings of the 4th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '77, pp.238-252, 1977.
DOI : 10.1145/512950.512973
URL : https://hal.archives-ouvertes.fr/hal-01108790

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

E. De-maria, F. Fages, A. Rizk, and S. Soliman, Design, optimization and predictions of a coupled model of the cell cycle, circadian clock, DNA repair system, irinotecan metabolism and exposure control under temporal logic constraints, Theoretical Computer Science, vol.412, issue.21, pp.4122108-2127, 2011.
DOI : 10.1016/j.tcs.2010.10.036
URL : https://hal.archives-ouvertes.fr/hal-01285815

F. Fages and A. Rizk, On temporal logic constraint solving for analyzing numerical data time series, Theoretical Computer Science, vol.408, issue.1, pp.55-65, 2008.
DOI : 10.1016/j.tcs.2008.07.004

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

A. Funahashi, Y. Matsuoka, A. Jouraku, M. Morohashi, N. Kikuchi et al., CellDesigner 3.5: A Versatile Modeling Tool for Biochemical Networks, Proceedings of the IEEE, pp.1254-1265, 2008.
DOI : 10.1109/JPROC.2008.925458

T. Daniel and . Gillespie, General method for numerically simulating stochastic time evolution of coupled chemical-reactions, Journal of Computational Physics, vol.22, pp.403-434, 1976.

E. Grafahrend-belau, F. Schreiber, M. Heiner, A. Sackmann, H. Björn et al., Modularization of biochemical networks based on classification of Petri net t-invariants, BMC Bioinformatics, vol.9, issue.1, p.9, 2008.
DOI : 10.1186/1471-2105-9-90

N. Hansen and A. Ostermeier, Completely Derandomized Self-Adaptation in Evolution Strategies, Evolutionary Computation, vol.9, issue.2, pp.159-195, 2001.
DOI : 10.1016/0004-3702(95)00124-7

D. Heitzler, G. Durand, N. Gallay, A. Rizk, S. Ahn et al., Competing G protein-coupled receptor kinases balance G protein and ??-arrestin signaling, Molecular Systems Biology, vol.3, issue.590, 2012.
DOI : 10.1038/msb.2012.22
URL : https://hal.archives-ouvertes.fr/hal-00776169

S. Hoops, S. Sahle, R. Gauges, C. Lee, J. Pahle et al., COPASI--a COmplex PAthway SImulator, Bioinformatics, vol.22, issue.24, pp.223067-3074, 2006.
DOI : 10.1093/bioinformatics/btl485

. De-an, J. Huang, R. Jiang, C. Huang, and . Cheng, Compiling program control flows into biochemical reactions, ICCAD'12: IEEE/ACM International Conference on Computer-Aided Design, 2012.

R. Huang, D. Huang, and H. Chiang, Jie-Hong Jiang, and François Fages. Species minimization in computation with biochemical reactions, IWBDA'13: Proceedings of the fifth International Workshop on Bio-Design Automation , Imperial College, 2013.

M. Hucka, The systems biology markup language (SBML): a medium for representation and exchange of biochemical network models, Bioinformatics, vol.19, issue.4, pp.524-531, 2003.
DOI : 10.1093/bioinformatics/btg015

M. Hucka, S. Hoops, S. M. Keating, L. N. Nicolas, S. Sahle et al., Systems biology markup language (SBML) level 2: Structures and facilities for model definitions, Nature Precedings, 2008.

J. R. Karr, J. C. Sanghvi, D. N. Macklin, M. V. Gutschow, J. M. Jacobs et al., A Whole-Cell Computational Model Predicts Phenotype from Genotype, Cell, vol.150, issue.2, p.389, 2012.
DOI : 10.1016/j.cell.2012.05.044

H. Kitano, Towards a theory of biological robustness, Molecular Systems Biology, vol.406, p.137, 2007.
DOI : 10.1038/msb4100179

H. Kitano, Systems Biology: A Brief Overview, Science, vol.295, issue.5560, pp.2951662-1664, 2002.
DOI : 10.1126/science.1069492

K. W. Kohn, Molecular Interaction Map of the Mammalian Cell Cycle Control and DNA Repair Systems, Molecular Biology of the Cell, vol.10, issue.8, pp.2703-2734, 1999.
DOI : 10.1091/mbc.10.8.2703

N. Le-novere, M. Hucka, H. Mi, S. Moodie, F. Schreiber et al., The systems biology graphical notation, Nature Biotechnology, issue.8, pp.27735-741, 2009.

H. Matsuno, A. Doi, M. Nagasaki, and S. Miyano, HYBRID PETRI NET REPRESENTATION OF GENE REGULATORY NETWORK, Biocomputing 2000, pp.338-349, 2000.
DOI : 10.1142/9789814447331_0032

H. Matsuno, Y. Tanaka, H. Aoshima, A. Doi, M. Matsui et al., Biopathways representation and simulation on hybrid functional petri net, In Silico Biology, vol.3, p.32, 2003.

F. Nabli, F. Fages, T. Martinez, and S. Soliman, A Boolean Model for Enumerating Minimal Siphons and Traps in Petri Nets, Proceedings of CP'2012, 18th International Conference on Principles and Practice of Constraint Programming, pp.798-814, 2012.
DOI : 10.1007/978-3-642-33558-7_57

M. Nagasaki, S. Onami, S. Miyano, and H. Kitano, Bio-calculus: Its concept, and an application for molecular interaction This book is a collection of poster papers presented at the RE- COMB, In Currents in Computational Molecular Biology Frontiers Science Series, vol.30, 2000.

C. Priami, A. Regev, W. Silverman, and E. Shapiro, 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

N. Venkatramana, M. L. Reddy, M. N. Mavrovouniotis, and . Liebman, Petri net representations in metabolic pathways, Proceedings of the 1st International Conference on Intelligent Systems for Molecular Biology (ISMB), pp.328-336, 1993.

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

A. Regev, W. Silverman, and E. Y. Shapiro, Representation and simulation of biochemical processes using the pi-calculus process algebra, Proceedings of the sixth Pacific Symposium of Biocomputing, pp.459-470, 2001.

A. Rizk, G. Batt, F. Fages, and S. Soliman, A general computational method for robustness analysis with applications to synthetic gene networks, Bioinformatics, vol.25, issue.12, pp.69-78, 2009.
DOI : 10.1093/bioinformatics/btp200
URL : https://hal.archives-ouvertes.fr/inria-00419708

A. Rizk, G. Batt, F. Fages, and S. Soliman, Continuous valuations of temporal logic specifications with applications to parameter optimization and robustness measures, Theoretical Computer Science, vol.412, issue.26, pp.2827-2839, 2011.
DOI : 10.1016/j.tcs.2010.05.008
URL : https://hal.archives-ouvertes.fr/hal-01431314

C. Rohr, W. Marwan, and M. Heiner, Snoopy--a unifying Petri net framework to investigate biomolecular networks, Bioinformatics, vol.26, issue.7, pp.974-975, 2010.
DOI : 10.1093/bioinformatics/btq050

A. Lee and . Segel, Modeling dynamic phenomena in molecular and cellular biology, 1984.

P. Senum and M. Riedel, Rate-independent constructs for chemical computation, PLOS One, vol.6, issue.6, 2011.

S. Soliman, Invariants and Other Structural Properties of Biochemical Models as a Constraint Satisfaction Problem, Algorithms for Molecular Biology, vol.7, issue.1, 2012.
DOI : 10.1007/BF01211911
URL : https://hal.archives-ouvertes.fr/hal-00784404

J. J. Tyson, Modeling the cell division cycle: cdc2 and cyclin interactions., Proceedings of the National Academy of Sciences, pp.7328-7332, 1991.
DOI : 10.1073/pnas.88.16.7328

J. Uhlendorf, A. Miermont, T. Delaveau, G. Charvin, F. Fages et al., Long-term model predictive control of gene expression at the population and single-cell levels, Proceedings of the National Academy of Sciences USA, pp.10914271-14276, 2012.
DOI : 10.1073/pnas.1206810109

I. Zevedei-oancea and S. Schuster, Topological analysis of metabolic networks based on petri net theory, In Silico Biology, vol.3, issue.29, 2003.