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Research Project: ML-Rules

  Multi-level modeling for cell biological systems

Abstract: 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.

  Research Project Information
Runtime: Aug 01, 2009 until Jul 31, 2012
Scientific staff: Dr.-Ing. Carsten Maus
Technical staff: Dipl. Inf. Stefan Rybacki
Student staff: M.Sc. Tobias Helms

Within this project, the formalism ML-DEVS for explicitly describing multi-level models has been already developed. A modeling study on RNA structure folding revealed that it is possible to describe cell-biological and molecular systems with ML-DEVS. However, it also turned out that the language concept which is based on the metaphor of reactive systems with asynchronous communication patterns hampers modeling of biochemical reactions. Therefore, the goal of this project is to incorporate the previously achieved results for multi-level modeling - including those results gained by Mathias John - into a formal language with well-defined syntax and semantics. Thereby, the syntax shall be defnined in an intuitive way, so that the language can be easily learned by domain experts from biology. A rule-based approach following the paradigm of chemical reaction definitions seems to be promising. Furthermore, the syntax shall explicitly support the description of hierarchical model structures and interactions between different levels. The semantics shall follow the well-established concept of continuous time Markov chains. To examine the applicability of the formal language concept for cellbiological systems, the project shall further include a detailed modeling study.