Interaction-based Programming in MGS

The modeling and simulation of morphogenetic phenomena require to take into account the coupling between the processes that take place in a space and the modification of that space due to those processes, leading to a chicken-and-egg problem. To cope with this issue, we propose to consider a growing structure as the byproduct of a multitude of interactions between its constitutive elements. An interaction-based model of computation relying on spatial relationships is then developed leading to an original style of programming implemented in the MGS programming language. While MGS seems to be at first glance a domain specific programming language, its underlying interaction-based paradigm is also relevant to support the development of generic programming mechanisms. We show how the specification of space independent computations achieves polytypism and we develop a direct interpretation of well-known differential operators in term of data movements.

[1]  W ReynoldsCraig Flocks, herds and schools: A distributed behavioral model , 1987 .

[2]  Paul Bourgine,et al.  Morphogenesis : origins of patterns and shapes , 2011 .

[3]  Olivier Michel,et al.  Declarative modeling of a neurulation-like process , 2007, Biosyst..

[4]  Julien Cohen Typing rule-based transformations over topological collections , 2003, Electron. Notes Theor. Comput. Sci..

[5]  Jean-Louis Giavitto,et al.  Rule-based programming for integrative biological modeling , 2008, Natural Computing.

[6]  Jean-Louis Giavitto,et al.  Interaction based simulation of dynamical system with a dynamical structure (DS)2 in MGS , 2011, SCSC 2011.

[7]  Jean-Louis Giavitto,et al.  Unconventional and Nested Computations in Spatial Computing , 2013, Int. J. Unconv. Comput..

[8]  Jean-Louis Giavitto,et al.  A Topological Framework for the Specification and the Simulation of Discrete Dynamical Systems , 2004, ACRI.

[9]  Pierre Barbier de Reuille,et al.  Computer simulations reveal novel properties of the cell-cell signaling network at the shoot apex in /Arabidopsis , 2005 .

[10]  Thomas Stützle,et al.  Ant Colony Optimization , 2009, EMO.

[11]  Sergey Verlan,et al.  Generalized Communicating P Systems Working in Fair Sequential Mode , 2011, Sci. Ann. Comput. Sci..

[12]  Tommaso Toffoli,et al.  Cellular automata machines - a new environment for modeling , 1987, MIT Press series in scientific computation.

[13]  Yiying Tong,et al.  Discrete differential forms for computational modeling , 2005, SIGGRAPH Courses.

[14]  Jean-Louis Giavitto,et al.  Interaction-Based Simulations for Integrative Spatial Systems Biology , 2011 .

[15]  M. Grandis Ordinary and directed combinatorial homotopy, applied to image analysic and concurrency , 2003 .

[16]  Prakash Panangaden,et al.  A Domain of Spacetime Intervals in General Relativity , 2005, Spatial Representation.

[17]  Jean-Louis Giavitto,et al.  Spatial Organization of the Chemical Paradigm and the Specification of Autonomic Systems , 2008, Software-Intensive Systems and New Computing Paradigms.

[18]  Craig W. Reynolds Flocks, herds, and schools: a distributed behavioral model , 1987, SIGGRAPH.

[19]  Bombelli,et al.  Space-time as a causal set. , 1987, Physical review letters.

[20]  John von Neumann,et al.  Theory Of Self Reproducing Automata , 1967 .

[21]  Daniel Le Métayer,et al.  Programming by multiset transformation , 1993, CACM.

[22]  Jean-Louis Giavitto,et al.  The Topological Structures of Membrane Computing , 2002, Fundam. Informaticae.

[23]  James R. Munkres,et al.  Elements of algebraic topology , 1984 .

[24]  A. Turing The chemical basis of morphogenesis , 1952, Philosophical Transactions of the Royal Society of London. Series B, Biological Sciences.

[25]  Glynn Winskel,et al.  Event Structures , 1986, Advances in Petri Nets.

[26]  Roland Carl Backhouse,et al.  Generic Programming: An Introduction , 1998, Advanced Functional Programming.

[27]  Jean-Pierre Jouannaud,et al.  Rewrite Systems , 1991, Handbook of Theoretical Computer Science, Volume B: Formal Models and Sematics.

[28]  R. Brockett Dynamical systems that sort lists, diagonalize matrices, and solve linear programming problems , 1991 .

[29]  A. Tucker,et al.  An Abstract Approach to Manifolds , 1933 .

[30]  Gheorghe Paun,et al.  Computing with Membranes: An Introduction , 1999, Bull. EATCS.

[31]  Jean-Louis Giavitto,et al.  MGS: a Programming Language for the Transformations of Topological Collections , 2011 .

[32]  A. Lindenmayer Mathematical models for cellular interactions in development. I. Filaments with one-sided inputs. , 1968, Journal of theoretical biology.

[33]  Olivier Michel,et al.  Topological computation of activity regions , 2013, SIGSIM PADS '13.

[34]  Alexander A. Stepanov,et al.  Generic Programming , 1988, ISSAC.

[35]  R. Sorkin Relativity Theory Does Not Imply that the Future Already Exists: A Counterexample , 2007, gr-qc/0703098.

[36]  D. Malament The class of continuous timelike curves determines the topology of spacetime , 1977 .

[37]  D. Gillespie Exact Stochastic Simulation of Coupled Chemical Reactions , 1977 .

[38]  Jean-Louis Giavitto,et al.  Topological rewriting and the geometrization of programming , 2008 .

[39]  Colin Smith,et al.  L-System Description of Subdivision Curves , 2003, Int. J. Shape Model..

[40]  Enzo Tonti,et al.  A Direct Discrete Formulation of Field Laws: The Cell Method , 2001 .

[41]  Roger Penrose,et al.  On the structure of causal spaces , 1967, Mathematical Proceedings of the Cambridge Philosophical Society.

[42]  Przemyslaw Prusinkiewicz,et al.  Stochastic P systems and the simulation of biochemical processes with dynamic compartments , 2008, Biosyst..

[43]  Luca Cardelli,et al.  On understanding types, data abstraction, and polymorphism , 1985, CSUR.

[44]  Michael Henle,et al.  A combinatorial introduction to topology , 1978 .

[45]  A. Lindenmayer Mathematical models for cellular interactions in development. II. Simple and branching filaments with two-sided inputs. , 1968, Journal of theoretical biology.

[46]  Olivier Michel,et al.  Using Rewriting Techniques in the Simulation of Dynamical Systems: Application to the Modeling of Sperm Crawling , 2005, International Conference on Computational Science.

[47]  Jean-Louis Giavitto,et al.  Declarative Mesh Subdivision Using Topological Rewriting in MGS , 2010, ICGT.

[48]  Pierre Barbier de Reuille Vers un modèle dynamique du méristème apical caulinaire d'Arabidopsis thaliana , 2005 .

[49]  L. Sander,et al.  Diffusion-limited aggregation , 1983 .

[50]  James Aspnes,et al.  An Introduction to Population Protocols , 2007, Bull. EATCS.

[51]  Johan Jeuring,et al.  Polytypic Programming , 1996, Advanced Functional Programming.

[52]  Prakash Panangaden,et al.  Causality in physics and computation , 2014, Theor. Comput. Sci..