C. Gleyse, R. Godin, F. Incitti, C. Képès, L. L. Lange et al., Hyperstructures, genome analysis and I-cells, Acta Biotheoretica, vol.50, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00827467

J. Giavitto, O. Michel, and J. Cohen, Pattern-matching and rewriting rules for group indexed data structures, ACM SIGPLAN Notices, vol.37, issue.12, pp.76-87, 2002.
DOI : 10.1145/636517.636529

J. Giavitto, O. Michel, and F. Delaplace, Declarative simulation of dynamicals systems: the 8 programming language and its application to the simulation of genetic networks, Biosystems, vol.68, issue.2-3, pp.2-3155, 2003.
DOI : 10.1016/S0303-2647(02)00093-X

J. Giavitto and O. Michel, Modeling the topological organization of cellular processes, Biosystems, vol.70, issue.2, pp.149-163, 2003.
DOI : 10.1016/S0303-2647(03)00037-6

J. Giavitto and O. Michel, Modeling the topological organization of cellular processes See http://www.physicsoflife.com/index. html. ( " Physics of Life " is an Elsevier electronic Journal selecting articles that have been published in 22 contributing journals from, Physics of Life Physics Biology, issue.3, 2003.

J. Giavitto, G. Malcolm, and O. Michel, Rewriting Systems and the Modelling of Biological Systems, Comparative and Functional Genomics, vol.5, issue.1, pp.95-99, 2004.
DOI : 10.1002/cfg.363

A. Spicher and O. Michel, Declarative modeling of a neurulation-like process, Biosystems, vol.87, issue.2-3, pp.281-288, 2006.
DOI : 10.1016/j.biosystems.2006.09.024

O. Michel, J. Banâtre, P. Fradet, and J. Giavitto, Challenging questions for the rationales of non-classical programming languages, International Journal of Unconventional Computing, 2006.

A. Spicher, O. Michel, M. Cieslak, J. Giavitto, and P. Prusinkiewicz, Stochastic P systems and the simulation of biochemical processes with dynamic compartments, Biosystems, vol.91, issue.3, 2007.
DOI : 10.1016/j.biosystems.2006.12.009
URL : https://hal.archives-ouvertes.fr/hal-00645928

[. Giavitto, O. Michel, J. Banâtre, and P. Fradet, Modèles de programmation non-conventionnels, Technique et Science Informatique, vol.23, pp.177-186, 2004.

A. Spicher and O. Michel, Repr??sentation et manipulation de structures topologiques dans un langage fonctionnel, Techniques et sciences informatiques, vol.26, issue.9, 2007.
DOI : 10.3166/tsi.26.1169-1194

O. Michel, J. Giavitto, and J. Sansonnet, A data-parallel declarative language for the simulation of large dynamical systems and its compilation, SMS-TPE'94: Software for Multiprocessors and Supercomputers Office of Naval Research USA & Russian Basic Research Foundation, pp.21-23, 1994.

J. Giavitto, O. Michel, J. Sansonnet, I. Takayasu, R. H. Jr et al., Group-based fields, Parallel Symbolic Languages and Systems (International Workshop PSLS'95), volume 1068 of Lecture Notes in Computer Sciences, pp.209-215, 1995.
DOI : 10.1007/BFb0023063

O. Michel, D. D. Vito, and J. Sansonnet, data-parallelism and data-flow, Intensional Programming II: Proc. of the 9th Int. Symp. on Lucid and Intensional Programming. World Scientific, 1996.

O. Michel, Introducing dynamicity in the data-parallel language 8 1/2, EuroPar'96 Parallel Processing, pp.678-686, 1996.
DOI : 10.1007/3-540-61626-8_89

O. Michel, A straightforward translation of D0L systems in the declarative data-parallel language 8 1/2, EuroPar'96 Parallel Processing, pp.714-718, 1996.
DOI : 10.1007/3-540-61626-8_94

D. De, V. , and O. Michel, Effective SIMD code generation for the high-level declarative data-parallel language 81/2, Euro Micro '96, pp.114-119, 1996.

J. Giavitto, D. D. Vito, and O. Michel, Semantics and compilation of recursive sequential streams in 81/2, Ninth International Symposium on Programming Languages, Implementations, Logics, and Programs (PLILP'97, pp.207-223, 1997.
DOI : 10.1007/BFb0033846

J. Giavitto, O. Michel, and F. Delaplace, Declarative simulation of dynamicals systems: the 8 programming language and its application to the simulation of genetic networks, Proceedings of IPCAT 2001 (Workshop on Information Processing in Cells and Tissues), 2001.
DOI : 10.1016/S0303-2647(02)00093-X

J. Giavitto and O. Michel, MGS, Pre-proceedings of WMC-CdeA 2001 (Workshop on Membrane Computing, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, MGS, Electronic Notes in Theoretical Computer Science, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, Declarative definition of group indexed data structures and approximation of their domains, Proceedings of the 3rd ACM SIGPLAN international conference on Principles and practice of declarative programming , PPDP '01, 2001.
DOI : 10.1145/773184.773201

J. Giavitto and O. Michel, Accretive rules in Cayley P systems, Preproceedings of WMC-CdeA 2002 (Workshop on Membrane Computing

J. Giavitto and O. Michel, Pattern-matching and Rewriting Rules for Group Indexed Data Structures In ACM -Rule'02, 2002.

J. Giavitto and O. Michel, Data Structure as Topological Spaces, Proceedings of the 3nd International Conference on Unconventional Models of Computation UMC02, 2002.
DOI : 10.1007/3-540-45833-6_12
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.106.9083

J. Giavitto, O. Michel, and J. Cohen, Accretive rules in cayley P systems, Membrane Computing, pp.319-338, 2002.

O. Michel and F. Jacquemard, An analysis of the needham-schroeder publickey protocol with MGS, Preproceedings of the Fifth workshop on Membrane Computing (WMC5), pp.295-315, 2004.

A. Spicher, O. Michel, and J. Giavitto, A Topological Framework for the Specification and the Simulation of Discrete Dynamical Systems, Sixth International conference on Cellular Automata for Research and Industry, pp.238-247, 2004.
DOI : 10.1007/978-3-540-30479-1_25

A. Spicher and O. Michel, Declarative modeling of a neurulation-like process, Sixth International Workshop on Information Processing in Cells and Tissues, 2005.
DOI : 10.1016/j.biosystems.2006.09.024

A. Spicher and O. Michel, Using Rewriting Techniques in the Simulation of Dynamical Systems: Application to the Modeling of Sperm Crawling, Fifth International Conference on Computational Science (ICCS'05), volume I, pp.820-827, 2005.
DOI : 10.1007/11428831_102

J. Giavitto, O. Michel, and A. Spicher, Computations in Space and Space in Computations, Unconventional Programming Paradigms (UPP'04), number LNCS 3566, pp.137-152, 2005.
DOI : 10.1007/11527800_11

A. Spicher, O. Michel, and J. Giavitto, Algorithmic Self-assembly by Accretion and by Carving in MGS, 7th International Conference on Artificial Evolution, 2005.
DOI : 10.1007/11740698_17
URL : https://hal.archives-ouvertes.fr/hal-00340495

]. Giavitto, J. Sansonnet, and O. Michel, Inférer rapidement la géometrie des collections, II.5.6 Publications in National Conferences (with review) [C1 Workshop on Static Analysis, 1992.

J. Giavitto and O. Michel, Calcul distribué de champs de données, Journées Francophones des Langages Applicatifs (JFLA99), Avoriaz, 1999.

J. Giavitto and O. Michel, Un cadre pour la définition récursive de données Mont Saint-Michel MGS : transformer des collections complexes pour la simulation en biologie, Journées Francophones des Langages Applicatifs (JFLA00) Journées Francophones des Langages Applicatifs (JFLA02), 2000.

A. Spicher and O. Michel, Stratégie d'application stochastique de r` egles de réécritures dans le langage MGS, Journées Francophones des Langages Applicatifs. INRIA, 2006.

A. Spicher and O. Michel, Manipulations de structures topologiques dans un langage déclaratif pour la simulation, 11ème Journées du GT " Animation et Simulation, 2004.
DOI : 10.3166/tsi.26.1169-1194

O. Michel and J. Giavitto, Amalgams: Names and name capture in a declarative framework, Technical Report, vol.32, 1998.

J. Giavitto and O. Michel, MGS, Electronic Notes in Theoretical Computer Science, vol.59, issue.4, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, The topological structures of membrane computing, 2001.

J. Giavitto, C. Godin, O. Michel, and P. Prusinkiewicz, Computational models for integrative and developmental biology, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00827466

J. Giavitto, O. Michel, and J. Cohen, Pattern-matching and rewriting rules for group indexed data structures, 2002.
DOI : 10.1145/636517.636529
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.100.9633

O. Michel, F. Jacquemard, and J. Giavitto, Three variations on the analysis of the needham-schroeder public-key protocol with MGS, 2004.

A. Spicher, O. Michel, and J. Giavitto, A Topological Framework for the Specification and the Simulation of Discrete Dynamical Systems, 2004.
DOI : 10.1007/978-3-540-30479-1_25

J. Giavitto, A. Spicher, and O. Michel, Topological rewriting and the geometrization of programming, Physica D: Nonlinear Phenomena, vol.237, issue.9, 2007.
DOI : 10.1016/j.physd.2008.03.039
URL : https://hal.archives-ouvertes.fr/hal-00340126

O. Michel and D. D. Vito, 8,5 un environnement de développement pour le langage 81/2, Journées du GDR Programmation, pp.22-23, 1994.

O. Michel and J. Giavitto, Typer une collection par la présentation d'un groupe, Journées du GDR Programmation, pp.23-24, 1995.

[. Michel, The 81/2 reference manual, 1995.

O. Michel, Les amalgames : un mécanisme pour la structuration et la construction incrémentielle de programmes déclaratifs, Journées du GDR Programmation, pp.20-22, 1996.

J. Giavitto, O. Michel, and J. Cohen, Une présentation du langage MGS. LaMI, université d' ´ Evry, 2002.

O. Michel, J. Banâtre, P. Fradet, and J. Giavitto, The Unconventional Programming Paradigms home page (UPP04) International workshop for " Challenges, Visions and Research Issues for New Programming Paradigms, pp.15-17, 2004.

A. Spicher and O. Michel, Integration and pattern-matching of topological structures in a functional language, International Workshop on Implementation and Application of Functional Languages (IFL04), 2004.

O. Michel and J. Giavitto, Incremental extension of a domain specific language interpreter In International Workshop on Implementation and Application of Functional Languages (IFL07) The draft proceedings will appear as a technical, 2007.

T. Michel, Représentations dynamiques de l'espace dans un langage déclaratif de simulation, II.5.9 Theses [, 1996.

A. Figure, 31: Four steps in the growth of a sheet of cells. The color of a cell is related to the concentration of the chemicals triggering the cell division (the darkest cells are about to divide)

A. Figure, 32: Screen dump of a type inference tool for a subset of MGS programs

H. Abelson, D. Allen, D. Coore, C. Hanson, G. Homsy et al., Amorphous computing, Communications of the ACM, vol.43, issue.5, pp.74-82, 2000.
DOI : 10.1145/332833.332842

A. Adamatzky, Reaction-diffusion and excitable processors: A sense of the unconventional. Parallel and Distributed Computing Practices, pp.113-132, 2001.

L. Adleman, Molecular computation of solutions to combinatorial problems, Science, vol.266, issue.5187, pp.1021-1025, 1994.
DOI : 10.1126/science.7973651

A. Edward, A. Ashcroft, R. Faustini, W. Jagannathan, and . Wadge, Multidimensional Programming, 1995.

K. P. Arvind and . Gostelow, Some relationships between asynchronous interpreters of a dataflow language, chapter in: Formal description of programming concepts, pp.95-119, 1977.

[. Auffray, S. Imbeaud, M. Roux-rouquié, and L. Hood, From functional genomics to systems biology: concepts and practices, Comptes Rendus Biologies, vol.326, issue.10-11, pp.10-11879, 2003.
DOI : 10.1016/j.crvi.2003.09.033

A. Asperti and G. Longo, Categories, Types, and Structures: An Introduction to Category Theory for the Working Computer Scientist. Foundations of Computing Series, 1991.

. Are06 and . Aresa, Reddetect -plant for landmine detection. Web, 2006.

A. Arnold, S??mantique des processus communicants, RAIRO. Informatique th??orique, vol.15, issue.2, pp.103-140, 1981.
DOI : 10.1051/ita/1981150201031
URL : http://archive.numdam.org/article/ITA_1981__15_2_103_0.pdf

A. Edward, W. W. Ashcroft, and . Wadge, Lucid, a nonprocedural language with iteration, Communications of the ACM, vol.20, issue.7, pp.519-526, 1977.

J. Backus, Can programming be liberated from the von Neumann style?: a functional style and its algebra of programs, Communications of the ACM, vol.21, issue.8, pp.613-641, 1978.
DOI : 10.1145/359576.359579

R. Carl-backhouse, STOP Summer School on constructive algorithmics, chapter An exploration of the Bird-Merteens formalism. Ameland, 1989.

G. Bracha and W. Cook, Mixin-based inheritance, OOPSLA ECOOP '90 Proceedings, pp.303-311, 1990.
DOI : 10.1145/97946.97982
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.156.4510

J. Boender, R. D. Cosmo, B. Durak, X. Leroy, F. Mancinelli et al., News from the EDOS project: improving the maintenance of free software distributions, Proceedings of the International Workshop on Free Software (IWFS'06), pp.199-207, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00154357

P. Barbier-de-reuille, Vers un modèle dynamique du méristème apical caulinaire d'Arabidopsis thaliana, 2005.

P. Barbier-de-reuille, I. Bohn-courseau, K. Ljung, H. Morin, N. Carraro et al., Computer simulations reveal properties of the cell-cell signaling network at the shoot apex in Arabidopsis, pp.1627-1632, 2006.
URL : https://hal.archives-ouvertes.fr/hal-00023247

D. P. Bertsekas, Distributed asynchronous computation of fixed points, Mathematical Programming, vol.12, issue.1, pp.107-120, 1983.
DOI : 10.1007/BF02591967

J. Banâtre, P. Fradet, J. Giavitto, and O. Michel, Unconventional Programming Paradigms, Revised Selected and Invited Papers of the International Workshop UPP, LNCS, vol.3566, 2004.

J. Banâtre, P. Fradet, and D. L. Métayer, Gamma and the Chemical Reaction Model: Fifteen Years After, Lecture Notes in Computer Science, vol.2235, pp.17-44, 2001.
DOI : 10.1007/3-540-45523-X_2

J. Banâtre, P. Fradet, and Y. Radenac, A Generalized Higher-Order Chemical Computation Model, Electronic Notes in Theoretical Computer Science, vol.135, issue.3, pp.3-13, 2006.
DOI : 10.1016/j.entcs.2005.09.016

J. Banâtre, P. Fradet, and Y. Radenac, Towards chemical coordination for grids, Proceedings of the 2006 ACM symposium on Applied computing , SAC '06, pp.445-446, 2006.
DOI : 10.1145/1141277.1141381

A. Ben-hur, T. Hava, and . Siegelmann, Computation in gene networks, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.14, issue.1, pp.145-151, 2004.
DOI : 10.1063/1.1633371

R. S. Bird, An Introduction to the Theory of Lists, Logic of Programming and Calculi of Discrete Design, NATO ASI Series, pp.217-245, 1987.
DOI : 10.1007/978-3-642-87374-4_1

[. Bergeron, G. Labelle, and P. Leroux, Combinatorial species and tree-like structures, volume 67 of Encyclopedia of mathematics and its applications, pp.0-521, 1997.

J. Banâtre and D. L. Metayer, A new computational model and its discipline of programming, 1986.

J. Banâtre and D. L. Metayer, GAMMA AND THE CHEMICAL REACTION MODEL: TEN YEARS AFTER, pp.3-41, 1996.
DOI : 10.1142/9781848161023_0001

M. L. Boas, Mathematical Methods in the Physical Sciences, 1983.

D. Boussié, Simulation en MGS du déplacement du spermatozo¨?despermatozo¨?de du nématode Ascaris Suum, 2004.

[. Brin and L. Page, The anatomy of a large-scale hypertextual Web search engine, Proc. 7th Int. World Wide Web Conf, pp.14-18, 1998.
DOI : 10.1016/S0169-7552(98)00110-X

J. Banâtre, Y. Radenac, and P. Fradet, Chemical specification of autonomic systems, Intelligent and Adaptive Systems and Software Engineering (IASSE), pp.72-79, 2004.

D. Thomas and C. , Studies in the Philosophy of Biology: Reductionism and Related Problems, chapter Downward causation " in hierarchically organized biological systems, pp.179-186, 1974.

R. Carlson, The Pace and Proliferation of Biological Technologies, Biosecurity and Bioterrorism: Biodefense Strategy, Practice, and Science, vol.1, issue.3, pp.203-214, 2003.
DOI : 10.1089/153871303769201851

[. Cardelli, Brane Calculi, Computational Methods in Systems Biology, pp.257-278, 2004.
DOI : 10.1016/S0020-0190(01)00214-9

J. Chory, J. R. Ecker, S. Briggs, M. Caboche, G. M. Coruzzi et al., National Science Foundation-Sponsored Workshop Report: ???The 2010 Project???Functional Genomics and the Virtual Plant. A Blueprint for Understanding How Plants Are Built and How to Improve Them, Plant Physiology, vol.123, issue.2, pp.423-426, 2000.
DOI : 10.1104/pp.123.2.423

]. K. Cha90 and . Chandy, Reasoning about continuous systems, Science of Computer Programming, vol.14, issue.23, pp.117-132, 1990.

[. Chen, A parallel language and its compilation to multiprocessor machines or VLSI, Proceedings of the 13th ACM SIGACT-SIGPLAN symposium on Principles of programming languages , POPL '86, pp.131-139, 1986.
DOI : 10.1145/512644.512656

[. Chen, Y. Il-choo, and J. Li, Crystal: Theory and Pragmatics of Generating Efficient Parallel Code, Parallel Functional Languages and Compilers, Frontier Series, chapter 7, pp.255-308

J. Cohen, Typing rule-based transformations over topological collections, Electronic Notes in Theoretical Computer Science, 2003.
DOI : 10.1016/S1571-0661(04)80676-5
URL : https://hal.archives-ouvertes.fr/hal-00442371

J. Cohen, Intégration des collections topologiques et des transformations dans un langage de programmation fonctionnel, 2004.
DOI : 10.3166/tsi.24.1081-1111

J. Cohen, Intégration des collections topologiques et des transformations dans un langage fonctionnel, 2004.

J. Cohen, Typage fort et typage souple des collections topologiques et des transformations, Journées Francophones des Langages Applicatifs, pp.37-54, 2004.
URL : https://hal.archives-ouvertes.fr/hal-00442431

E. Melvin and . Conway, Design of a separable transition-diagram compiler, Communication of the ACM, vol.6, issue.7, pp.396-408, 1963.

D. Coore, Botanical Computing: A Developmental Approach to Generating Interconnect Topologies on an Amorphous Computer, 1999.

E. N. Delsinne, Structures de données indexées par un groupe, isomorphismes de gbf abéliens et extensions aux structures automatiques, 2002.

J. André-de-hon, F. Giavitto, and . Gruau, Computing Media and Languages for Space-Oriented Computation, number 06361 in Dagsthul Seminar Proceedings, Dagsthul, pp.3-8, 2006.

[. Dershowitz and J. Jouannaud, Handbook of Theoretical Computer Science, volume B, chapter Rewrite systems, pp.244-320, 1990.

E. Mathieu-desbrun, Y. Kanso, and . Tong, Discrete differential forms for computational modeling, Discrete differential geometry: an applied introduction, pp.39-54, 2006.

[. Dershowitz and Z. Manna, Proving termination with multiset orderings, Communications of the ACM, vol.22, issue.8, pp.465-476, 1979.
DOI : 10.1145/359138.359142
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.145.8728

E. Kim and . Drexler, Molecular engineering: An approach to the development of general capabilities for molecular manipulation, Proc. Nat. Acad. Sci. USA, pp.5275-5278, 1981.

D. Duggan and C. Sourelis, Mixin modules, Proceedings of the 1996 ACM SIGPLAN International Conference on Functional Programming, pp.262-273, 1996.

B. Ducourthial, Les réseaux associatifs ? un modèle de programmationàprogrammation`programmationà parallélisme de données, pour algorithmes et données irréguliers, ` a primitives de calcul asynchrones, 1999.

[. Dittrich, J. Ziegler, and W. Banzhaf, Artificial Chemistries???A Review, Artificial Life, vol.17, issue.3, pp.225-275, 2001.
DOI : 10.1162/106454601753138998

. Talcott, Pathway Logic, Electr. Notes Theor. Comput. Sci, p.71, 2002.
DOI : 10.1007/978-3-540-68894-5_2

[. Endy, Foundations for engineering biology, Nature, vol.42, issue.7067, pp.438449-453, 2005.
DOI : 10.1038/nature04342

E. Engeler, Combinatory differential fields, Theoretical Computer Science, vol.72, issue.2-3, pp.119-131, 1990.
DOI : 10.1016/0304-3975(90)90031-C

M. Eigen and P. Schuster, The Hypercycle, The Science of Nature, vol.44, issue.Suppl. 2, 1979.
DOI : 10.1007/978-3-642-66784-8_18

. Farge, Mechanical Induction of Twist in the Drosophila Foregut/Stomodeal Primordium, Current Biology, vol.13, issue.16, pp.1365-1377, 2003.
DOI : 10.1016/S0960-9822(03)00576-1

A. A. Faustini, An operational semantics for pure dataflow, Automata, languages and programing: ninth colloquium, pp.212-224, 1982.
DOI : 10.1007/BFb0012771

W. Fontana and L. W. Buss, the arrival of the fittest " : Toward a theory of biological organization, Bulletin of Mathematical Biology, 1994.

R. P. Feynman, There's plenty of room at the bottom ? an invitation to enter a new field of physics, Engineering and Science, 1960.

P. François and V. Hakim, Design of genetic networks with specified functions by evolution in silico, Proceedings of the National Academy of Sciences, vol.101, issue.2, pp.580-585, 2004.
DOI : 10.1073/pnas.0304532101

G. Fischer, The software technology of the 21st century: From software reuse to collaborative software design Software Engineers Association , Japan, International Symposium on Future Software Technology, pp.1-8, 2001.

M. Fisher, G. Malcolm, and R. Paton, Spatio-logical processes in intracellular signalling, Biosystems, vol.55, issue.1-3, pp.83-92, 2000.
DOI : 10.1016/S0303-2647(99)00086-6

W. Fontana, Pulling strings, Science, issue.5805, pp.3141552-1553, 2006.

F. L. , F. , and S. Patarin, MLdonkey, a multi-network peer-to-peer file-sharing program, 2007.
URL : https://hal.archives-ouvertes.fr/inria-00071789

R. P. Gabriel, Objects have failed ? notes for a debate Debate at OOPSLA, 2002.

M. Gardner, Mathematical Games, Scientific American, vol.223, issue.4, pp.120-123, 1970.
DOI : 10.1038/scientificamerican1070-120

F. Gaubert, Simulation stochastique et modélisation de chimie artificielle dans le langage MGS, 2005.

J. Giavitto, D. D. Vito, and O. Michel, Semantics and compilation of recursive sequential streams in 81/2, Ninth International Symposium on Programming Languages, Implementations , Logics, and Programs (PLILP'97, pp.207-223, 1997.
DOI : 10.1007/BFb0033846

J. Giavitto, C. Godin, O. Michel, and P. Prusinkiewicz, Computational models for integrative and developmental biology, 2002.
URL : https://hal.archives-ouvertes.fr/hal-00827466

J. Giavitto, C. Godin, O. Michel, and P. Prusinkiewicz, Modelling and Simulation of biological processes in the context of genomics, chapter Computational Models for Integrative and Developmental Biology, Hermes, 2002.

J. Giavitto, Typing geometries of homogeneous collection, 2nd Int. workshop on array manipulation, 1992.

J. Giavitto, Scientific Report for the habilitation, Research Report, 1226.

J. Giavitto, A fixed point approach to the resolution of array equations, Fixed Points in Computer Science (FICS'2000), 2000.

J. Giavitto, A framework for the recursive definition of data structures, Proceedings of the 2nd ACM SIGPLAN international conference on Principles and practice of declarative programming , PPDP '00, pp.45-55, 2000.
DOI : 10.1145/351268.351275

J. Giavitto, Invited talk: Topological collections, transformations and their application to the modeling and the simulation of dynamical systems, Rewriting Technics and Applications (RTA'03), volume LNCS 2706 of LNCS, pp.208-233, 2003.

J. Giavitto, Modelling and simulation of biological processes in the context of genomics, chapter On The biochemical abstract machine BIOCHAM Comments on a presentation of François Fages to the thematic school, pp.175-176, 2004.

J. Gibbons, An introduction to the Bird-Meertens formalism, New Zealand Formal Program Development Colloquium Seminar, 1994.

W. Wayt and . Gibbs, Synthetic life, Scientific American, vol.290, issue.5, pp.74-81, 2004.

T. Daniel and . Gillespie, Exact stochastic simulation of coupled chemical reactions, J. Phys. Chem, vol.81, issue.25, pp.2340-2361, 1977.

E. Goubault and T. P. Jensen, Homology of higher dimensional automata
DOI : 10.1007/BFb0084796

J. Giavitto and O. Michel, MGS, Electronic Notes in Theoretical Computer Science, vol.59, issue.4, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, MGS, Electronic Notes in Theoretical Computer Science, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, MGS, Pre-proceedings of WMC-CdeA, 2001.
DOI : 10.1016/S1571-0661(04)00293-2
URL : https://hal.archives-ouvertes.fr/hal-00769284

J. Giavitto and O. Michel, Data Structure as Topological Spaces, Proceedings of the 3nd International Conference on Unconventional Models of Computation UMC02, pp.137-150, 2002.
DOI : 10.1007/3-540-45833-6_12

J. Giavitto and O. Michel, Pattern-matching and rewriting rules for group indexed data structures, ACM Sigplan Workshop RULE'02, pp.55-66, 2002.

J. Giavitto and O. Michel, The topological structures of membrane computing, Fundamenta Informaticae, vol.49, pp.107-129, 2002.

J. Giavitto and O. Michel, Modeling the topological organization of cellular processes, Biosystems, vol.70, issue.2, pp.149-163, 2003.
DOI : 10.1016/S0303-2647(03)00037-6

J. Giavitto and O. Michel, Molecular Computational Models: Unconventional Approaches, chapter Modeling Developmental Processes in MGS Idea Group Publishing, pp.150-189, 2004.

J. Giavitto, O. Michel, and J. Cohen, Pattern-matching and rewriting rules for group indexed data structures, ACM SIGPLAN Notices, vol.37, issue.12, pp.76-87, 2002.
DOI : 10.1145/636517.636529

J. Giavitto, O. Michel, and J. Cohen, Pattern-matching and rewriting rules for group indexed data structures, 2002.

J. Giavitto, O. Michel, J. Cohen, and A. Spicher, Computations in Space and Space in Computations, Unconventional Programming Paradigms, pp.137-152, 2005.
DOI : 10.1007/11527800_11

J. Giavitto, G. Malcolm, and O. Michel, Rewriting Systems and the Modelling of Biological Systems, Comparative and Functional Genomics, vol.5, issue.1, pp.95-99, 2004.
DOI : 10.1002/cfg.363

[. Gachet, C. Mauras, P. Quinton, and Y. Saouter, Alpha du centaur, Proceedings of the 3rd international conference on Supercomputing , ICS '89, pp.235-243, 1989.
DOI : 10.1145/318789.318815
URL : https://hal.archives-ouvertes.fr/inria-00075606

J. Giavitto, O. Michel, and J. Sansonnet, Group-based fields, Parallel Symbolic Languages and Systems (International Workshop PSLS'95), pp.209-215, 1995.
DOI : 10.1007/BFb0023063

E. Goubault, Geometry and concurrency: a user's guide, Mathematical Structures in Computer Science, vol.10, issue.4, pp.411-425, 2000.
DOI : 10.1017/S0960129500003133

A. Carl, D. S. Gunter, and . Scott, Handbook of Theoretical Computer Science, Semantic Domains, pp.633-674, 1990.

F. Scott, S. Gilbert, and . Sarkar, Embracing complexity: Organicism for the 21st century, Developmental Dynamics, vol.219, pp.1-9, 2000.

J. Giavitto and A. Spicher, Systems Self-Assembly: multidisciplinary snapshots, chapter Simulation of self-assembly processes using abstract reduction systems, 2006.

[. Head, Formal language theory and DNA: An analysis of the generative capacity of specific recombinant behaviors, Bulletin of Mathematical Biology, vol.15, issue.6, pp.737-759, 1987.
DOI : 10.1007/BF02481771

M. Henle, A combinatorial introduction to topology, 1994.

J. Y. Hung, W. Gao, and J. C. Hung, Variable structure control: a survey, IEEE Transactions on Industrial Electronics, vol.40, issue.1, pp.2-22, 1993.
DOI : 10.1109/41.184817

T. Hogg and B. A. Huberman, Controlling smart matter, Smart Materials and Structures, vol.7, issue.1, p.1, 1998.
DOI : 10.1088/0964-1726/7/1/001
URL : http://arxiv.org/abs/cond-mat/9611024

W. Daniel and . Hillis, The Connection Machine, 1985.

N. Anil and . Hirani, Discrete exterior calculus, 2003.

[. Hammarlund and B. Lisper, On the relation between functional and data parallel programming languages, Proceedings of the conference on Functional programming languages and computer architecture , FPCA '93, pp.210-222, 1993.
DOI : 10.1145/165180.165211

[. Hashimoto and A. Ohori, A typed context calculus, Theoretical Computer Science, vol.266, issue.1-2, 1996.
DOI : 10.1016/S0304-3975(00)00174-2

J. H. Holland, Genetic Algorithms and the Optimal Allocation of Trials, SIAM Journal on Computing, vol.2, issue.2, pp.88-105, 1973.
DOI : 10.1137/0202009

J. H. Holland, Adpatation in Natural and Artificial Systems, 1975.

[. Horn and . Research, Autonomic computing: IBM's perspective on the state of information technology, 2001.

B. [. Harper, J. Rosen, and . White, The Growth and Form of Modular Organism, 1986.

J. Hughes, Why Functional Programming Matters, The Computer Journal, vol.32, issue.2, pp.98-107, 1989.
DOI : 10.1093/comjnl/32.2.98

M. Jammer, Concepts of space ? the history of theories of space in physics, 1993.

H. Jönsson, M. G. Heisler, B. E. Shapiro, E. M. Meyerowitz, and E. Mjolsness, An auxin-driven polarized transport model for phyllotaxis, Proceedings of the National Academy of Sciences, pp.1633-1638, 2006.
DOI : 10.1073/pnas.0509839103

Y. Jullian, Conception et développement d'unéditeurunéditeur graphique de filtre pour MGS. Master's thesis, 2005.

G. Kahn, The semantics of a simple language for parallel programming, Information processing, pp.471-475, 1974.

C. Kaleta, Outils de visualisation pour la simulation de systèmes dynamiquesà dynamiquesà structure dynamique, 2007.

S. Kaufman, The Origins of Order: Self-Organization and Selection in Evolution, 1995.

N. Kam, D. Harel, H. Kugler, R. Marelly, A. Pnueli et al., Formal Modeling of C. elegans Development: A Scenario-Based Approach, First International Workshop on Computational Methods in Systems Biology, pp.4-20, 2003.
DOI : 10.1007/3-540-36481-1_2

H. Kitano, S. Hamahashi, and S. Luke, Project: An Initial Report, Artificial Life, vol.16, issue.12, pp.141-156, 1998.
DOI : 10.1098/rstb.1986.0056

H. Kobayashi, M. Kaern, M. Araki, K. Chung, S. Timothy et al., Programmable cells: Interfacing natural and engineered gene networks, Proceedings of the National Academy of Sciences, vol.101, issue.22, pp.8414-8419, 2004.
DOI : 10.1073/pnas.0402940101
URL : http://www.ncbi.nlm.nih.gov/pmc/articles/PMC420408

M. Richard, R. E. Karp, and . Miller, Properties of a model of parallel computations : determinacy, termination and queuing, SIAM Journal of Applied Mathematics, vol.14, pp.1390-1411, 1966.

R. M. Karp, R. E. Miller, and S. Winograd, The Organization of Computations for Uniform Recurrence Equations, Journal of the ACM, vol.14, issue.3, pp.563-590, 1967.
DOI : 10.1145/321406.321418

T. Knight, R. Rettberg, L. Chan, D. Endy, R. Shetty et al., Idempotent vector design for the standard assembly of biobricks, 2007.

J. Peter and . Landin, The next 700 programming languages, Communications of the ACM, vol.9, issue.3, pp.157-166, 1966.

V. Larue, Structures de données indexées par un groupe : représentation graphique et extension au cas non abélien, 2002.

[. Ledoux, ´ Etude et spécifications formelles de l'arrondi d'objets géométriques

[. Leone, Programming language research

[. Lee and D. P. Friedman, Quasi-static scoping, Proceedings of the 20th ACM SIGPLAN-SIGACT symposium on Principles of programming languages , POPL '93, pp.479-492, 1993.
DOI : 10.1145/158511.158706

[. Lee and D. P. Friedman, Enriching the lambda calculus with contexts: toward a theory of incremental program construction, International Conference on Functional Programming, 1996.

]. A. Lin68 and . Lindenmayer, Mathematical models for cellular interaction in development, Parts I and II, Journal of Theoretical Biology, vol.18, pp.280-315, 1968.

B. Lisper, Data parallelism and functional programming, Proc. ParaDigme Spring School on Data Parallelism, 1996.
DOI : 10.1007/3-540-61736-1_50

J. Bruce and . Maclennan, Replication, sharing, deletion, lists, and numerals: Progress on universally programmable intelligent matter, 2002.

]. Mac03, . Mit-project, and . Mac, The Amorphous Computing Home page, 2003.

P. Maes, A bottom-up mechanism for behavior selection in an artificial creature, Proceedings of the first international conference on simulation of adaptative behavior (SAB, 1991.

V. Manca, Logical string rewriting, Theoretical Computer Science, vol.264, issue.1, pp.25-51, 2001.
DOI : 10.1016/S0304-3975(00)00212-7

[. Mann, Hyperstructures et modélisation de chimie artificielle dans le langage MGS, 2004.

O. Michel, J. Banâtre, P. Fradet, and J. Giavitto, Challenging questions for the rationales of non-classical programming languages, International Journal of Unconventional Computing, 2006.

H. Meinhardt, Models of Biological Pattern Formation, 1982.

[. Meijer, M. M. Fokkinga, and R. Paterson, Functional programming with bananas, lenses, envelopes and barbed wire, 5th ACM Conference on Functional Programming Languages and Computer Architecture, pp.124-144, 1991.
DOI : 10.1007/3540543961_7
URL : http://citeseerx.ist.psu.edu/viewdoc/summary?doi=10.1.1.41.125

O. Michel and J. Giavitto, Amalgams: Names and name capture in a declarative framework, 1998.

O. Michel and J. Giavitto, Incremental extension of a domain specific language interpreter, 19th International Symposium on Implementation and Application of Functional Languages, pp.27-29, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00945006

O. Michel, Design and implementation of 81/2, a declarative data-parallel language, 1995.

O. Michel, Design and implementation of 812: A declarative data-parallel language, Computer Languages, vol.22, issue.2-3, pp.165-179, 1996.
DOI : 10.1016/S0096-0551(96)00012-4

O. Michel, Introducing dynamicity in the data-parallel language 81/2, p.96

O. Michel, Les amalgames : un mécanisme pour la structuration et la construction incrémentielle de programmes déclaratifs, Journées du GDR Programmation, pp.20-22, 1996.

O. Michel, Représentations dynamiques de l'espace dans un langage déclaratif de simulation, 1996.

O. Michel, A straightforward translation of d0l systems in the declarative dataparallel language 81, Euro-Par '96: Proceedings of the Second International Euro-Par Conference on Parallel Processing, pp.714-717, 1996.

O. Michel and F. Jacquemard, An Analysis of a Public-Key Protocol with Membranes Natural Computing Series, pp.283-302, 2005.

S. Warren, W. Mcculloch, and . Pitts, A logical calculus of ideas immanent in nervous activity, Bulletin of Mathematical Biophysics, vol.5, pp.115-133, 1943.

P. John, T. Mylopoulos, and . Pavlidis, On the topological properties of quantized spaces. i. the notion of dimension, Journal of the ACM (JACM), vol.18, pp.238-246, 1971.

J. Maynard-smith, Shaping Life: Genes, Embryos and Evolution, 1999.

R. Milner and S. Stepney, Nanotechnology: Computer science opportunities and challenges, Submission by the UK Computing Research Committee to the Nanotechnology Working Group of the Royal Society and the Royal Academy of Engineering, 2003.

[. Mjolsness, D. H. Sharp, and J. Reinitz, A connectionist model of development, Journal of Theoretical Biology, vol.152, issue.4, pp.429-454, 1991.
DOI : 10.1016/S0022-5193(05)80391-1

A. Oram, Peer-to-Peer: Harnessing the Power of Disruptive Technologies, 2001.

S. Outerbah, Introduction d'une notion de référence distante dans un formalisme de capture de noms et implémentation d'une plate-forme d'expérimentation. Master's thesis, 1998.

P. Gheorghe, Computing with membranes, Journal of Computer and System Sciences, vol.1, issue.61, pp.108-143, 2000.

P. Gheorghe, From cells to computers: Computing with membranes (p systems)

P. Gheorghe, From cells to computers: Computing with membranes (P systems)

Y. Prusinkiewicz, B. Erasmus, L. D. Lane, E. Harder, and . Coen, Evolution and Development of Inflorescence Architectures, Science, vol.316, issue.5830, pp.3161452-1456, 2007.
DOI : 10.1126/science.1140429

L. Perret, Intégration des types de données algébriques dans MGS. Master's thesis, 2005.

A. Prusinkiewicz, J. S. Lindenmayer, and . Hanan, The Algorithmic Beauty of Plants, 1990.
DOI : 10.1007/978-1-4613-8476-2

[. Prusinkiewicz and A. , Modeling plant morphogenesis, Current Opinion in Plant Biology, vol.9, issue.1, pp.83-88, 2006.
DOI : 10.1016/j.pbi.2005.11.015

[. Prusinkiewicz, Pattern Formation in Biology, Vision, and Dynamics , chapter Paradigms of pattern formation: Towards a computational theory of morphogenesis, World Scientific, 2000.

P. Quinton, S. Rajopadhye, and D. Wilde, Deriving imperative code from functional programs, Proceedings of the seventh international conference on Functional programming languages and computer architecture , FPCA '95, pp.36-44, 1995.
DOI : 10.1145/224164.224177

P. Quinton, An introduction to systolic architectures, Proceedings of the Advanced Course on Future Parallel Computers, pp.387-400, 1986.
DOI : 10.1007/3-540-18203-9_13

E. Rauch, Discrete, amorphous physical models, International Journal of Theoretical Physics, vol.42, issue.2, pp.329-348, 2003.
DOI : 10.1023/A:1024455602163

A. Richard, Modèle formel pour les réseaux de régulation génétique & Influence des circuits de rétroaction, 2006.

[. Róka, One-way cellular automata on Cayley graphs, Theoretical Computer Science, vol.132, issue.1-2, pp.259-290, 1994.
DOI : 10.1016/0304-3975(94)90236-4

[. Róka, The firing squad synchronization problem on Cayley graphs, Lecture Notes in Computer Science, vol.969, p.402, 1995.
DOI : 10.1007/3-540-60246-1_146

E. M. Dae-kyun-ro, M. Paradise, K. J. Ouellet, K. L. Fisher, J. M. Newman et al., Production of the antimalarial drug precursor artemisinic acid in engineered yeast, Nature, pp.440940-943, 2006.

W. K. Paul, N. Rothemund, E. Papadakis, and . Winfree, Algorithmic selfassembly of DNA Sierpinski triangles, Preliminary Proceedings of DNA Computing , 9th international Workshop on DNA-Based Computers, pp.1-4, 2003.

[. Rozenberg and A. Salomaa, Lindenmayer Systems, 1992.
DOI : 10.1007/978-3-642-58117-5

S. Stepney, S. L. Braunstein, J. A. Clark, A. M. Tyrrell, A. Adamatzky et al., Journeys in non-classical computation II: initial journeys and waypoints. Parallel Algorithms Appl, pp.97-125, 2006.

J. Segard, Modèles de morphogénèse biologique dans un langage déclaratif de simulation, 1997.

R. S. Smith, S. Guyomarc-'h, T. Mandel, D. Reinhardt, C. Kuhlemeier et al., A plausible model of phyllotaxis, Proceedings of the National Academy of Sciences, vol.103, issue.5, pp.1301-1306, 2006.
DOI : 10.1073/pnas.0510457103

L. Guy, W. D. Steele, and . Hillis, Connection machine LISP: Fine grained parallel symbolic programming, Proceedings of the 1986 ACM Conference on LISP and Functional Programming, pp.279-297, 1986.

A. Spicher and O. Michel, Integration and pattern-matching of topological structures in a functional language In International Workshop on Implementation and Application of Functional Languages, 2004.

A. Spicher and O. Michel, Declarative modeling of a neurulation-like process, Biosystems, vol.87, issue.2-3, pp.281-288, 2006.
DOI : 10.1016/j.biosystems.2006.09.024

A. Spicher and O. Michel, Représentation et manipulation de structures topologiques dans un langage fonctionnel. Technique et Science Informatique, 2007.

A. Spicher, O. Michel, M. Cieslak, J. Giavitto, and P. Prusinkiewicz, Stochastic p systems and the simulation of biochemical processes with dynamic compartments. BioSystems, page in press, 2007.
URL : https://hal.archives-ouvertes.fr/hal-00645928

A. Spicher, O. Michel, and J. Giavitto, A Topological Framework for the Specification and the Simulation of Discrete Dynamical Systems, Sixth International conference on Cellular Automata for Research and Industry (ACRI'04), 2004.
DOI : 10.1007/978-3-540-30479-1_25

A. Spicher, O. Michel, and J. Giavitto, Rewriting and Simulation -Application to the Modeling of the Lambda Phage Switch, volume Modélisation de systèmes biologiques complexes dans le contexte de la génomique, chapter Modeling of the Lambda Phage Switch, Genopole, 2006.

A. Soto, La causalité biologique : ´ emergence et interaction dans la morphogenèse normale et cancéreuse. Ecole thématique " Logique et interaction : vers une géométrie de la cognition, 2006.

A. Spicher, Typage et compilation de filtrage de chemins dans des collections topologiques, 2003.

A. Spicher, Transformation de collections topologiques de dimension arbitraire ? ApplicationàApplication`Applicationà la modélisation de systèmes dynamiques, 2006.

A. Spicher, Transformation de collections topologiques de dimension arbitraires ApplicationàApplication`Applicationà la modélisation de systèmes dynamiques, 2006.

[. Szybalski and A. Skalka, Nobel-prizes and restriction enzymes, Gene, 1978.

E. [. Sulston, J. G. Schierenberg, J. N. White, and . Thomson, The embryonic cell lineage of the nematode Caenorhabditis elegans, Developmental Biology, vol.100, issue.1, pp.64-119, 1983.
DOI : 10.1016/0012-1606(83)90201-4

G. Seelig, D. Soloveichik, D. Y. Zhang, and E. Winfree, Enzyme-Free Nucleic Acid Logic Circuits, Science, vol.314, issue.5805, pp.3141585-1588, 2006.
DOI : 10.1126/science.1132493

I. Stewart, Four encounters with Sierpinski's gasket, Mathematical Intelligencer, vol.17, pp.52-64, 1995.
DOI : 10.1007/bf03024718

[. Strachey, Fundamental concepts in programming languages, Notes. International Summer School in Computer Programming, 1967.

J. Gerald and . Sussman, Robust design through diversity (position paper), Workshop on Amorphous Computing, p.99, 1999.

P. Schröder and D. Zorin, Subdivision for modeling and animation. volume SIGGRAPH'98 course notes, 1998.

G. Lawrence, H. J. Tesler, and . Enea, A language design for concurrent processes, AFIPS Conference Proceedings, pp.403-408, 1968.

R. Thomas, Logical analysis of systems comprising feedback loops, Journal of Theoretical Biology, vol.73, issue.4, pp.631-656, 1978.
DOI : 10.1016/0022-5193(78)90127-3

[. Thonnérieux, Réalisation d'une interface graphique pour le traitement des sorties du programme MGS, IIE, 2003.

S. Tixeuil, Vers l'auto-stabilisation des systèmessystèmesà grande echelle HabilitationàHabilitation`Habilitationà Diriger les Recherches, 2006.

R. Thomas and M. Kaufman, Multistationarity, the basis of cell differentiation and memory. I. Structural conditions of multistationarity and other nontrivial behavior, Chaos: An Interdisciplinary Journal of Nonlinear Science, vol.11, issue.1, pp.170-179, 2001.
DOI : 10.1063/1.1350439

[. Toffoli and M. Norman, Cellular Automata Machine, 1987.

A. M. Turing, The chemical basis of morphogenesis, Phil. Trans. Roy. Soc. of London, Series B: Biological Sciences, issue.237, pp.37-72, 1952.

M. Stanislas and . Ulam, On some mathematical problems connected with patterns of growth of figures, Proc. Symposia Appl, pp.215-224, 1962.

. Var99, J. Francisco, and . Varela, Principle of Biological Autonomy

J. Von-neumann, Theory of Self-Reproducing Automata, 1966.

R. Weiss, S. Basu, S. Hooshangi, A. Kalmbach, D. Karig et al., Genetic circuit building blocks for cellular computation, communications, and signal processing, Natural Computing, vol.2, issue.1, pp.43-84, 2003.

E. Wiedmer, Computing with infinite objects, Theoretical Computer Science, vol.10, issue.2, pp.133-155, 1980.
DOI : 10.1016/0304-3975(80)90011-0

L. Wittgenstein, Logisch-philosophischen Abhandlung, Annalen der Naturphilosophie, pp.185-262, 1921.

R. Weiss and T. Knight, Engineered communications for microbial robotics, DNA: International Workshop on DNA-Based Computers, 2000.
DOI : 10.1007/3-540-44992-2_1

L. Wolpert, J. Smith, T. Jessell, P. Lawrence, E. Robertson et al., Principles of development, 1998.

[. Yang and Y. Choo, Data fields as parallel programs, Proceedings of the Second International Workshop on Array Structure, 1992.

[. Yokobayashi, R. Weiss, and F. H. Arnold, Directed evolution of a genetic circuit, Proceedings of the National Academy of Sciences, vol.99, issue.26, pp.16587-16591, 2002.
DOI : 10.1073/pnas.252535999

B. R. Evans, J. R. Mielenz, R. C. Hopkins, and M. W. Adams, High-yield hydrogen production from starch and water by a synthetic enzymatic pathway, PLoS ONE, vol.2, issue.5, p.456, 2007.