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© Oxford University Press

METASIM: object-oriented modelling of cell regulation

J.Stoffers Huub , L.L.Sonnhammer Erik , J.F.Blommestijn Gerard , J.H.Raat Nicolaas 2,1 and V.Westerhoff Hans 2,3

Department of Biophysics Plesmanlaan 121, NL-1066 OCAmsterdam
2Division of Molecular Biology, Netherlands Cancer Institute Plesmanlaan 121, NL-1066 CX Amsterdam
3E.C.Slater Institute for Biochemical research. University of Amsterdam The Netherlands

1Present address: Department of Cell Physiology, KUN, PO Box 9101, NL-6500 HB Nijmegen, The Netherlands

Enzymatic processes and substances are modelled as distinct objects, belonging to a limited number of classes. A set of class definitions in C{boxplus}{boxplus}is presented that constitutes an object-oriented programming platform. The latter supports ‘biological’ data types and functions and facilitates simulation of metabolic and regulatory pathways in living cells. To compute the time-evolution, Euler or Runge–Kutta methods are used, though the latter method compromises a stria object-oriented philosophy. As an example, histone gene expression during embryogenesis ofXenopus laevis is modelled. This object-oriented programming system forms a modelling ‘language’ which is readily understood by both biochemists and programmers. It allows biologial problems to be programmed more easily and correctly and brings the program closer to the biological reality, hence making it more meaningful to bioscientists. Moreover, it can readily be extended to new models by class derivation.

Received on July 10, 1991; accepted on February 14, 1992

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