Keywords: Systems Biology, Discrete-Event Modeling and Simulation, Multi-Level Modeling and Simulation

The project is aimed at the development of modeling and simulation methods taking the specific challenges of Systems Biology into account and that support a description and analysis at different levels of detail. Therefore, concrete models shall be generated. Thus, the project combines research on modeling and simulation methodology and research on generating cellular models.

The goal of this project is to develop a modeling and simulation framework which is sufficiently flexible and modular to support teaching of modeling and simulation methods, research on modeling and simulation methods, applications in diverse areas, and modeling and simulation of complex, heterogenous systems. In the beginning the project was intended to provide solutions for multi agent models and simulations but we dropped this specialization as most aspects of modelling and simulation are more common. Thus the result is still usable for multi agent models but by no means restricted to such models.

Parallele verteilte Simulation deliberativer Agenten

The goal of the collaborative project of the University of Rostock and the Georgia Institute of Technology is to develop efficient and flexible discrete event simulation methods for cell-biological systems. The focus of the project will be on parallel optimistic approaches and the utilization of grid technology for execution. The project will built on existing and ongoing work on designing component-based, flexible simulators, multi-level, modeling and simulation in Systems Biology and on efficient, parallel, distributed simulation of large scale systems, and grid technology.

The goal of the project is to develop and combine suitable algorithms to support an effective and efficient simulation of Brownian dynamics Simulations. The results of the micro-scale simulations shall provide additional insights into biological phenomena that cannot be treated at higher levels of abstraction (e.g. molecular crowding).

JAMES has been the first implementation of a simulation framwork for the DynDEVS formalism.

Keywords: Discrete-event / hybrid simulation, Grid-computing, Multi-resolution simulation, Stochastic Simulation Algorithm (SSA), Gillespie Algorithm, Next Subvolume Method

Biological systems are hierarchically organized into different levels, e.g. molecules, compartments, cells, tissues, and organs. Thereby, dynamic processes at any level may be influenced by processes at higher or lower levels of the hierarchy. In this project, methods are developed that make formal modeling of biological multilevel systems more accessible to domain experts.

Means that help a better integration between wet-lab and dry-lab experiments shall be developed, e.g., in the area of parameter estimation, or model validation.