Towards a Virtual Biological Laboratory

For a system-level understanding of living cells, a quantitative representation of these systems involving mathematical models and corresponding computer tools is required. Our approach focuses on a modeling concept which relies upon modular structuring of cellular systems focusing strongly on the biomolecular structure of these systems. Mathematical submodels for functional units comprising metabolism and regulation can be aggregated in a hierarchical way to obtain more complex modules. In the Virtual Biological Laboratory, the process modeling tool ProMoT contains an object-oriented knowledge base with reusable modeling entities and enables a purely symbolical model development process via a graphical user interface. The simulation environment Diva then uses the model library for dynamic simulation, parameter estimation and model analysis. Two examples of models of complex regulatory networks in Escherichia coli and in Saccharomyces cerevisiae are given to demonstrate the usefulness of this approach. It can provide a framework for straightforward development of virtual representations for cellular systems