Research Project: ESCeMMO

Efficient Simulation of Cell-Biological Multi-Level Models


This project shall advance the current state of the art in the effective modeling of cell biological systems, the efficient execution of multi-level models, and the evaluation of multi-level modeling languages and algorithms.

Research Project Information

   Runtime:    Since Apr 01, 2013
   Project coordination:    Prof. Dr. rer. nat. habil. Adelinde M. Uhrmacher
   Scientific staff:    M. Sc. Tobias Helms; M. Sc. Bioinformatics Fiete Haack
   Dipl.-Math Christina Kossow
   Student staff:   Jan Max Kreutzer; Marcus Szymanski;
   Steffen Mentel; Maria Pierce; Till K√∂ster;
   Florian Thonig; Eric B√ľchner; Robert Kohlen
   Contractor:   DFG (DFG GEPRIS Link)

Over the last years, diverse modeling languages have been developed to facilitate multi-level modeling in cell biology. However, using these languages still involves considerable simulation efforts, which hampers their wider applicability to simulation studies. Our aim is to develop more efficient execution strategies that take properties and requirements of multi-level models into account. To reach this goal, methods for on-demand configuration, parallelization, and approximation will receive particular attention. The research will be based on ML-RULES, a rule-based multi-level modeling language realized in the plug-in based modeling and simulation framework JAMES II, which will be refined and extended as part of the project. The impact of the developed methods in supporting multi-level modeling and simulation will be evaluated by both performance experiments and user studies. The results of the project will enrich the portfolio of modeling languages, execution methods, and evaluation strategies in the area of multi-level modeling and simulation.