Declarative simulation of dynamicals systems: The 8 1/2 programming language and its application to the simulation of genetic networks

BioSystems

Volumn 68, Issue 2-3, 2003, Pages 155-170

  Giavitto, Jean Louis ^a   Michel, Olivier ^a   Delaplace, Franck ^a  

^a UNIVERSITY OF EVRY   (France)

Author keywords

Biological processes; Collection; Declarative programming languages; Simulation of dynamical systems; Stream

Indexed keywords

BIOLOGICAL PROCESSES; MODELING;

COMPUTER PROGRAM; CONFERENCE PAPER; GENETIC ENGINEERING; MATHEMATICAL ANALYSIS; MOLECULAR MODEL; SIMULATION;

EID: 0037320929     PISSN: 03032647     EISSN: None     Source Type: Journal    
DOI: 10.1016/S0303-2647(02)00093-X     Document Type: Conference Paper

References (42)

1. Arvind, Brock, J.D., 1983. Streams and managers. In: Proceedings of the 14th IBM Computer Science Symposium.
2. Bard J., Lauder L. How well does turing's theory of morphogenesis work. Journal of Theoretical Biology. 45:1974;501-531.
3. Blelloch G. Scans as primitive parallel operations. IEEE Transactions on Computers. 38:(11):1989;1526-1538.
4. Blelloch G., Sabot G.W. Compiling collection-oriented languages onto massively parallel computers. Journal of Parallel and Distributed Computing. 8:1990;119-134.
5. Chen, T., He, H., Church, G., 1999. Modeling gene expression with differential equations. In: Proceedings of the Pacific Symposium on Biocomputing'99, pp. 112-123.
6. De Vito D., Michel O. Effective SIMD code generation for the high-level declarative data-parallel language 8 1 2 . EuroMicro'96. 1996;114-119 IEEE Computer Society.
7. Dittrich, P., 2001. Artificial chemistry webpage. URL http://www.cs.uni-dortmund.de/achem .
8. Fontana, W., Buss, L., 1996. The barrier of objects: from dynamical systems to bounded organizations. In: Casti, J., Karlqvist, A. (Eds.), Boundaries and Barriers. Addison-Wesley, pp. 56-116.
9. Giavitto, J.-L., 1992. Typing geometries of homogeneous collection. In: Second International Workshop on Array Manipulation (ATABLE), Montréal.
10. Giavitto, J.-L., 1999. Scientific repport for the hdr. Ph.D. thesis. LRI, Université de Paris-Sud, Centre d'Orsay, Research Report 1226.
11. Giavitto, J.-L., 2000. A framework for the recursive definition of data structures. In: ACM-Sigplan Second International Conference on Principles and Practice of Declarative Programming (PPDP'00). ACM-Press, Montréal, pp. 45-55.
12. n. In: EuroPar'98 Parallel Processing. Lecture Notes in Computer Science.
13. Giavitto J.-L., Michel O., Sansonnet J.-P. Group based fields. Takayasu L., Halstead R.H.J., Queinnec C. Parallel Symbolic Languages and Systems (International Workshop PSLS'95), Lecture Notes in Computer Science. 1068:1995;209-215 Springer, Beaune, France.
14. Hofestädt R. A petri net application of metabolic processes. Jounal of System Analysis Modelling and Simulation. 16:1994;113-122.
15. Hudak, P., et al., 1996. Report on the programming language HASKELL a non-strict, purely functional language, version 1.3. CS Department, Yale University.
16. Jayaraman B. Implementation of subset-equational program. Journal of Logic Programming. 12:1992;299-324.
17. Koster C.G., Lindenmayer A. Discrete and continuous models for heterocyst diffrentiation in growing filaments of blue-green bacteria. Acta Biotheoretica. 36:1987;249-273.
18. Lindenmayer A. Mathematical models for cellular interactions in development parts I and II. Journal of Theoretical Biology. 18:1968;280-315.
19. Lindenmayer A., Jürgensen H. Grammars of development; discrete-state models for growth, differentiation, and gene expression in modular organisms. Ronzenberg G., Salomaa A. Lindenmayer Systems, Impacts on Theoretical Computer Science, Computer Graphics and Developmental Biology. 1992;3-21 Springer.
20. Lisper, B., 1993. On the relation between functional and data-parallel programming languages. In: Proceedings of the Sixth International Conference on Functional Languages and Computer Architectures, ACM, ACM Press.
21. Maes P. A bottom-up mechanism for behavior selection in an artificial creature. Book B. Proceedings of the First International Conference on Simulation of Adaptative Behavior. 1991;MIT Press.
22. Mahiout, A., Giavitto, J.-L., 1994. Data-parallelism and data-flow: automatic mapping and scheduling for implicit parallelism. In: Franco-British meeting on Data-parallel Languages and Compilers for portable parallel computing, Villeneuve d'Ascq, 20 avril.
23. McAdams, H., Shapiro, L., 1995. Circuit simulation of genetic networks. Science, 269.
24. Michel O. A straightforward translation of D0L Systems in the declarative data-parallel language 8 1 2 . Bougé L., Fraigniaud P., Mignotte A., Robert Y. EuroPar'96 Parallel Processing, Lecture Notes in Computer Science. 1123:1996;714-718 Springer.
25. Michel, O., Giavitto, J., 1994. Design and implementation of a declarative data-parallel language. In: Post-ICLP'94 Workshop W6 on Parallel and Data Parallel Execution of Logic Programs. Uppsala University, Computing Science Department, S. Margherita Liguria, Italy.
26. Michel, O., Giavitto, J.-L., 1998a. Amalgams: Names and name capture in a declarative framework. Tech. Rep. 32, LaMI-Université d'Évry Val d'Essonne, also available as LRI Research-Report RR-1159.
27. Michel, O., Giavitto, J.-L., 1998b. A declarative data parallel programming language for simulations. In: Proceedings of the Seventh International Colloquium on Numerical Analysis and Computer Science with Applications. Plovdiv, Bulgaria.
28. Michel, O., Giavitto, J.-L., Sansonnet, J.-P., 1994. A data-parallel declarative language for the simulation of large dynamical systems and its compilation. In: SMS-TPE'94: Software for Multiprocessors and Supercomputers, Office of Naval Research USA & Russian Basic Research Foundation, Moscow, 21-23 September, pp. 103-111.
29. Matsuno, H., Doi, A., Nagasaki, M., Miyano, S., 1999. Hybrid Petri Net representation of gene regulatory network. In: Proceedings of the Pacific Symposium on Biocomputing'99, pp. 112-123.
30. Mitchinson G.J., Wilcox M. Rule governing cell division in anaeba. Nature. 239:1972;110-111.
31. NSF, 1991. Grand challenges: high performance computing and communications. A Report by the Committee on Physical, Mathematical and Engineering Sciences, NSF/CISE, 1800 G Street NW, Washington, DC 20550.
32. Paun, G., 2000. From cells to computers: computing with membranes (p systems). In: Workshop on Grammar Systems. Bad Ischl, Austria.
33. Prusinkiewicz P., Hanan J. L systems: from formalism to programming languages. Ronzenberg G., Salomaa A. Lindenmayer Systems, Impacts on Theoretical Computer Science, Computer Graphics and Developmental Biology. 1992;193-211 Springer.
34. Schwartz, J.T., Dewar, R.B.K., Dubinsky, E., Schonberg, E., 1986. Programming with sets: and introduction to SETL, Springer.
35. Sipelstein J.M., Blelloch G. Collection-oriented languages. Proceedings of the IEEE. 79:(4):1991;504-523.
36. Smith G.D. Numerical solution of partial differential equations: finite difference methods. Oxford Applied Mathematics and Computing series. 1985;Oxford University Press.
37. Thieffry, D., Thomas, R., 1998. Qualitative analysis of gene networks. In: Proceedings of the Pacific Symposium on Biocomputing'98, pp. 77-88.
38. Thieffry D., Roméro D. The modularity of biological regulatory networks. Biosystem. 50:1999;49-59.
39. TMC, 1986. The Essential LISP Manual. Thinking Machines Corporation, Cambridge, MA.
40. Tofooli T.N.M. Cellular Automata Machine. 1987;MIT Press, Cambridge, MA.
41. Wadge W.W., Ashcroft E.A. LUCID - a formal system for writing and proving programs. SIAM Journal on Computing. 3:1976;336-354.
42. Weaver, D., Workman, C., Stormo, G., 1999. Modeling regulatory networks with weight matrices. In: Proceedings of the Pacific Symposium on Biocomputmg'99, pp. 112-123.