METASIM: object-oriented modelling of cell regulation

Enzymatic processes and substances are modelled as distinct objects, belonging to a limited number of classes. A set of class definitions in C⊞⊞is presented that constitutes an object-oriented programming platform. The latter supports ‘biological’ data types and functions and facilitates simulation...

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Bibliographic Details
Published in:Bioinformatics 1992-10, Vol.8 (5), p.443-449
Main Authors: Huub, J.Stoffers, Erik, L.L.Sonnhammer, Gerard, J.F.Blommestijn, Nicolaas, J.H.Raat, Hans, V.Westerhoff
Format: Article
Language:English
Subjects:
Biological and medical sciences
Cell metabolism, cell oxidation
Cell physiology
Cells - metabolism
Computer Simulation
Fundamental and applied biological sciences. Psychology
Models, Biological
Molecular and cellular biology
Programming Languages
Software
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Summary:Enzymatic processes and substances are modelled as distinct objects, belonging to a limited number of classes. A set of class definitions in C⊞⊞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.
ISSN:1367-4803
0266-7061
1460-2059
DOI:10.1093/bioinformatics/8.5.443