Discrete Event Simulation for a Better Understanding of Metabolite Channeling - A System Theoretic Approach

• Authors: Daniela Degenring;Mathias Röhl;Adelinde Uhrmacher
• Venue: CMSB '03 Proceedings of the First International Workshop on Computational Methods in Systems Biology
• Year: 2003

Typically differential equations are employed to simulate metabolic processes. To develop a valid continuous model based on differential equations requires accurate parameter estimations; an accuracy which is often difficult to achieve, due to the lacko f data. In addition processes in metabolic pathways, e.g. metabolite channeling, seem to be of a rather qualitative and discrete nature. With respect to the available data and to the perception of the underlying system a discrete rather than a continuous approach to modeling and simulation seems more adequate. However, a discrete approach does not necessarily imply a more abstract view on the system. If we move from macro to micro and multi-level modeling, aspects of subsystems and their interactions, which have been only implicitly represented, are now explicit part of the model. Based on the simulation environment James we started exploring phenomena of metabolite channeling on different levels of abstractions. James is a discrete event simulation system and supports a modular hierarchical composition of models, the change of modeling structure during simulation, and a distributed, parallel execution of models.