Towards an Object-Oriented Framework for the Modeling of Integrated Metabolic Processes

1 I n t r o d u c t i o n Scientific research in biotechnology and biochemical engineering which influences other domains such as metabolic engineering and medicine is increasingly interested in the development of methodologies and computer-aided tools for mathematical modeling and dynamic simulation of metabolic processes. This is due to the fact tha t mathematical modeling and dynamic simulation proceed to s tudy more and more complex processes on different levels of detail. Thus, different mathematical models and simulations can be found for metabolic processes. However, the majori ty of the published models and simulation studies describe either metabolic reactions or a single metabolic pathway or exclusively the indirect regulation of them at the level of transcription, translation, and gene expression (e.g [16]). A smaller number describe metabolic pathways as a set of biochemical reactions together with their interactions with the processes of gene expression and protein biosynthesis (e.g. [11]). Novel and established methods of molecular biology allow the isolation, sequence analysis and functional interpretation of genes. These methods lead to an exponential growth of the available biological data. To handle large and different kinds of such da ta sets various database systems (e.g. GENBANK, EMBL, SWISSPROT) are available. These systems represent data about sequenced genes and enzymes of different organisms. For the interpretation of DNA sequence data, software tools based upon such database systems are still under development (see e.g. [7]). Detailed mathematical models of bacterial metabolism require different kinds of data, e.g. da ta about all sequenced gene structures and amino acids, enzymes and