LiSEB: a language for modeling living systems with APL2

ABSTRACT

The paper discusses the design and implementation of LiSEB, a class-based language built on top of APL2 to respond to challenges posed by modelling living systems from a medical point of view. LiSEB capitalises on several features of APL and on some lessons learned from its history. Living systems are modelled as open systems: environments in which concurrent mobile autonomous agents interact. Modelling of these properties required extensions of traditional object-oriented paradigms and of their previous translations under APL: a) every object performs a sequence of actions dynamically modified to adapt to circumstances; b) a new policy of message management is introduced uniformly encompassing broadcast and directly addressed communication. An example of a simulation using LiSEB illustrates these concepts.

REFERENCES

• ACM92: ACM SIGBio Newsletter, "Special edition on biologically motivated computing", vol.12, n.2, 1992
• ACM93: Communications of the ACM, "Special issue on Concurrent Object Programming", vol. 33, n.9, 1993
• Alf89: Manuel Alfonseca, Object oriented programming in APL2, ACM SIGAPL APL Quote Quad, v.19 n.4, p.6-11, Aug. 1989
• BBDS78: P.Berry, J.Bartoli, C.Dell'Aquila, V.Spadavecchia, "APL & insight" Pleasantville, N.Y., APL Press, 1978
• BMP90: P. Bottoni , P. Mussio , M. Protti, Definition of image interpretation strategies in APL, ACM SIGAPL APL Quote Quad, v.20 n.4, p.50-60, July 1990
• BMP91: P. Bottoni , M. Protti , P. Mussio, An APL rule-based system architecture for image interpretation strategies, ACM SIGAPL APL Quote Quad, v.21 n.4, p.51-61, Aug. 1991
• BMP94: P. Bottoni , P. Mussio , M. Protti, Metareasoning in the determination of image interpretation strategies, Pattern Recognition Letters, v.15 n.2, p.177-190, Feb. 1994 [doi>10.1016/0167-8655(94)90047-7]
• BSB89: M. v. Baaren , F. H. D. v. Batenberg , H. P. T. v. d. Star, Discrete simulation by APL-GPSS: the best of two worlds, ACM SIGAPL APL Quote Quad, v.19 n.4, p.12-22, Aug. 1989
• CS92: F.Celada, P. Seiden "A Computer Model for Cellular Interaction in The Immune System" Immunology Today 1992 Vol.13, No.2, pp 56-62
• DFCF92: A.Drogoul, J.Ferber, B.Corbara, D.Fresneau "A behavioral simulation model for the study of emergent social structures" in F.J.Varela, P.Bourgine Towards a practice of autonomous systems, MIT Press, 1992, pp.171-178
• Dio84: N.Dioguardi, "I1 fegato, un sistema aperto", Masson, Milano, 1984
• GC90: Nicholas Carriero , David Gelernter, How to write parallel programs: a first course, MIT Press, Cambridge, MA, 1990
• Gey88: A.Geyer-Schulz, "Fuzzy rule-based expert systems" in APL Techniques in expert systems, J.R,Kraemer, P.C.Berry eds., SIGAPL - Syracuse University, 1988
• GF71: B.L.Gordon, D.K.Ford, "Essential of immunology" F.A.Davis Company Philadelphia 1971
• Gfe89: M. Gfeller, Object oriented programming in AIDA APL, ACM SIGAPL APL Quote Quad, v.19 n.4, p.164-168, Aug. 1989
• GHT89: A. Geyer-Schulz , A. Taudes , J. Mitlöhner, An APL-tutoring adventure game, ACM SIGAPL APL Quote Quad, v.19 n.4, p.148-157, Aug. 1989
• GR83: A.Goldberg, D.Robson, "Smalltalk80", Addison-Wesley, 1983
• GS87: Jean Jacques Girardot , Sega Sako, An object oriented extension to APL, Proceedings of the international conference on APL: APL in transition, p.128-137, May 10-14, 1987, Dallas, Texas, United States
• Ive80: Kenneth E. Iverson, Notation as a tool of thought, Communications of the ACM, v.23 n.8, p.444-465, Aug. 1980 [doi>10.1145/358896.358899]
• MP92: Zohar Manna , Amir Pnueli, The temporal logic of reactive and concurrent systems, Springer-Verlag New York, Inc., New York, NY, 1992
• MPB91: P.Mussio, M.Pietrogrande, F.Brambilla, C.Caserta, A.Cefalo, M.T.Randetti, P.Bottoni, N.Dioguardi, "Modeling of biological and medical systems: a systemic strategy", Biosystems, vol.26, pp. 31-43, 1992
• MT89: M.D.Mesarovic, Y.Takahara "Abstract Systems Theory" Springer-Verlag, 1989
• Mus90: P.Mussio, "The state space approach to system representation as a language for medical universe: the liver case", V.D'Amato, C.Maccheroni, eds., Dynamic Analyisis Of Complex Systems, pp.257-267, Franco Angeli, 1990
• NR87: Constantin Virgil Negoita , Anca L. Ralescu, Simulation, Knowledge-Based Computing, and Fuzzy Statistics, John Wiley & Sons, Inc., New York, NY, 1987
• Per91: A.S.Perelson, "immunol. Review", vol.ll0, pp. 5-36, 1991
• PM89: G.Papaspyropoulos, D.Maritas, "Parallel Discrete Event Simulation with SIMULA", Elsevier, 1989
• PNSB92: R.C.Paton, H.S.Nwana, M.J.R .S have, T.J.M.Bench-Capon, "Computing at the tissue/organ level (with particular reference to the liver)", in F.J.Varela, P.Bourgine Towards a practice of autonomous systems, MIT Press, 1992, pp.411-420
• PSBM90: M.Pietrogrande, B.Sagramoso, P.Bottoni, P.Mussio,N.Dioguardi, "Utilization of systemic models for the study of pathogenesis, chimical picture and therapy of disease. Case study: crioglobulinemia", in Dynamic Analysis of complex systems pp.274-278, eds V.D'Ambra, C.Maccheroni, Franco Angeli, 1990
• SB86: Mark Stefik , Daniel Bobrow, Object-oriented programming: Themes and variations, AI Magazine, v.6 n.4, p.40-62, Winter 1986
• vB69: " L. von Bertalanffy, "General system theory", Braziller, New York, 1969
• Weg87: Peter Wegner, The object-oriented classification paradigm, Research directions in object-oriented programming, MIT Press, Cambridge, MA, 1987

INDEX TERMS

Primary Classification:
  D. Software
  D.3 PROGRAMMING LANGUAGES
      D.3.2 Language Classifications

          Nouns: APL

General Terms:
Languages