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Institute of Bio- and Geosciences

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The modeling and simulation group supports the IBG-1 and our partners in academia and industry with model based data analysis, experimental design and process optimization. State of the art models and computational tools are developed and applied in close collaboration with experimental researchers from biology, biochemistry and bioengineering sciences. The modeling and simulation group provides expertise in mathematics, computer science, and related subjects for data driven and quantitative studies of microorganisms and biochemical processes. A major task is the analysis and optimization of biochemical networks with following core competencies (primarily supervised by Dr. Katharina Nöh):

  1. Stationary and non-stationary 13C metabolic flux analysis (13C MFA)

  2. Integrative network modeling and systems analysis

  3. Live cell image analysis

The modeling and simulation group is also involved in processes analysis and design (primarily supervised by Dr. Eric von Lieres). Current projects are concerned with:

  1. Automation of lab robotic high throughput experiments

  2. Packed bed and membrane chromatography

  3. Microfluidic lab on chip systems

Typical projects address parameter identification, error estimation, experimental design, and model validation. Usually an experimental cycle is entered in which models are applied for focusing experimental work and iteratively refined on basis of the experimental outcome. Many projects require advanced numerical methods and high performance computing, in particular when Monte Carlo simulations, global optimization, or computational fluid dynamics are performed. The modeling and simulation group offers mathematical consulting to our internal and external partners.

Specific computational tools are designed for modeling, simulating and visualizing biochemical systems and for improving interdisciplinary communication. Several open source projects are distributed to the scientific community on the ModSim GitHub page. Following software packages are of particular importance:

  1. 13CFLUX2 for quantifying intracellular fluxes by analysis of carbon labeling experiments

  2. Chromatography Analysis and Design Toolkit (CADET).

  3. The visualization software OMIX® developed at the ModSim group is now maintained by Omix Visualization GmbH & Co. KG.