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© Oxford University Press

Object-oriented programming for the biosciences

W. Wiechert 2, B. Joksch , R. Wittig , A. Hartbrich , T. Höner and M. Möllney 1

Institut für Biotechnologie, Forschungszentrum Jülich 52425 Jülich, Germany
1Abteilung Theorelische Biologie, Universitdt Bonn Kirschallee 1, 53115 Bonn, Germany

1To whom correspondence should be addressed. Email: w.weichert{at}kfa-juelich.de

The development of software systems for the biosciences is always closely connected to experimental practice. Programs must be able to handle the inherent complexity and heterogeneous structure of biological systems in combination with the measuring equipment. Moreover, a high degree of flexibility is required to treat rapidly changing experimental conditions. Object-oriented methodology seems to be well suited for this purpose. It enables an evolutionary approach to software development that still maintains a high degree of modularity. This paper presents experience with object-oriented technology gathered during several years of programming in the fields of bioprocess development and metabolic engineering. It concentrates on the aspects of experimental support, data analysis, interaction and visualization. Several examples are presented and discussed in the general con text of the experimental cycle of knowledge acquisition, thus pointing out the benefits and problems of object-oriented technology in the specific application field of the biosciences. Finally, some strategies for future developments are described.

Received on February 20, 1995; accepted on June 9, 1995

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