title: Object-oriented programming for the biosciences.
abstract: 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 context 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 development are described.
authors.affiliation: Institut für Biotechnologie, Forschungszentrum Jülich, Germany. w.weichert@kfajuelich.de
authors.forename: W
authors.initials: W
authors.lastname: Wiechert
authors.forename: B
authors.initials: B
authors.lastname: Joksch
authors.forename: R
authors.initials: R
authors.lastname: Wittig
authors.forename: A
authors.initials: A
authors.lastname: Hartbrich
authors.forename: T
authors.initials: T
authors.lastname: Höner
authors.forename: M
authors.initials: M
authors.lastname: Möllney
mesh_terms: D000465:Algorithms; D001695:Biology; D003196:Computer Graphics; D003201:Computers; D003627:Data Interpretation, Statistical; D016208:Databases, Factual; D005069:Evaluation Studies as Topic; D005821:Genetic Techniques; D009682:Magnetic Resonance Spectroscopy / Q000379:methods; D012106:Research; D012984:Software / Q000592:standards; D009626:Terminology as Topic; D014584:User-Computer Interface