Subproject: Post Phd project V
Research project context: »X-topics which link the other research projects«
|Experiment Design and Simulation Execution for Biologists|
|Research Project Information||Subproject Information|
Runtime: 2006-10-01 until 2011-03-31
Project coordination: Prof. Dr. rer. nat. habil. Andreas Heuer; Prof. Dr. rer. nat. habil. Adelinde M. Uhrmacher; Prof. Dr. med. habil. Arndt Rolfs; Prof. Dr. rer. nat. Dieter G. Weiss
The overall goal of this project is to better support biologists in conducting simulation experiments with JAMES II, the major modeling and simulation software used and developed in the graduate school. At first, biologists should be supported in designing experiments that are valid, efficient to compute, and yield meaningful results. These simulation experiments should be specified in a general format that fosters reuse and allows a prior analysis of experiment properties (e.g. regarding their structure).
Secondly, the experiments need to be executed by the most suitable combination of algorithms. This combination of algorithms should be selected automatically, since users are easily overwhelmed by the plethora of available algorithms.
Finally, the outcomes of simulation experiments have to be analyzed carefully, particularly regarding their validity. This motivates enhanced methods for experiment design (so that, e.g., model validity regarding certain aspects can be ascertained) and also additional support for the presentation of the experiment results.
Dependencies on other projects:
- The simulation experiments shall help to understand models of the biological systems of interest (e.g., multi-level models, stochastic models with continuous space, or mathematical models).
- The design and specification of experiments should base on the notion of modeling and simulation workflows.
- The execution of experiments by suitable algorithm combinations requires simulation algorithm selection, a methodology which needs further enhancements in this context (e.g., to provide automatic selection for other kinds of JAMES II algorithms).
- The output analysis (and parts of the experiment design) should incorporate methods for experimental model validation.
- Familiarization with the concrete biological questions that could be answered by simulation experiments.
- Enhancing the support for result presentation in JAMES II.
- Investigating the automatic selection of auxiliary algorithms.