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Methods in Computational Systems Biology

Dr. Sven Sahle

The Group of Methods in Computational Systems Biology specializes in methodological research for mathematical modeling in biology, creating and assessing numerical methods.
Our primary project, COPASI, aids in creating, simulating, and analyzing biochemical reaction network models, which are widely adopted by researchers. Additionally, we offer spatial kinetic model simulation software, excelling in stochastic simulations, ODEs, PDE-based spatial modeling, optimization methods, and constraint-based modeling. Our work intersects with the Biomedical Computer Vision group, which develops advanced methods for computer-based analysis of biological and medical images. They focus on deriving quantitative information from microscopy image data, achieving top-ranking results in international competitions on particle and cell tracking. These methods have been successfully applied in various applications, bridging the gap between experimental image data and quantitative modeling.

Research Strategy

The research group Biomedical Computer Vision develops methods and algorithms for computer-based analysis of biological and medical images. A main aim is to derive quantitative information about cellular and subcellular structures from microscopy image data. We have developed a wide spectrum of novel advanced image analysis methods for cell segmentation and tracking, particle detection and tracking, non-rigid image registration, vessel segmentation, and landmark localization comprising deep learning methods, model-based methods, and probabilistic methods. Top-ranking results in international competitions on particle and cell tracking were achieved. The developed methods have been successfully used in different applications to study virus infection, cell migration and division, and the genome architecture in cooperation with biomedical partners, particularly with research groups at BioQuant. Our work is important to bridge the gap between experimental image data and quantitative modeling.

User interface of the spatial simulator software ( The software generates a computational mesh from a preprocessed image of a hepatocyte (upper panel) and displays simulation results (lower panel).


Project Leader

Dr. Sven Sahle

Phone:  +49 (0)6221 54-51272


Room:  BioQuant, Im Neuenheimer Feld 267

Selected Publications

SBML Level 3: an extensible format for the exchange and reuse of biological models >

Sarah M Keating, Dagmar Waltemath, Matthias König, Fengkai Zhang, Andreas Dräger, Claudine Chaouiya, Frank T Bergmann, Andrew Finney, Colin S Gillespie, Tomáš Helikar, Stefan Hoops, Rahuman S Malik-Sheriff, Stuart L Moodie, Ion I Moraru, Chris J Myers, Aurélien Naldi, Brett G Olivier, Sven Sahle & SBML Level 3 Community members 

Mol Syst Biol.2020 Aug;16(8):e9110

Spatial modeling reveals nuclear phosphorylation and subcellular shuttling of YAP upon drug-induced liver injury

Lilija Wehling,Liam Keegan, Paula Fernández-Palanca, Reham Hassan, Ahmed Ghallab, Jennifer Schmitt,Yingyue Tang, Maxime Le Marois, Stephanie Roessler,Peter Schirmacher, Ursula Kummer, Jan G Hengstler, Sven Sahle and Kai Breuhahn 

eLife. 2022; 11: e78540.

COPASI and its applications in biotechnology

Frank T Bergmann, Stefan Hoops, Brian Klahn, Ursula Kummer, Pedro Mendes, Jürgen Pahle, Sven Sahle 

J Biotechnol.2017 Nov 10:261:215-220