A01 - Domain-specific languages for developing multi-scale, spatio-temporal, bio-chemical models and their application

Summary of the work programme

To study cellular responses to external electrical fields, executing and relating simulation studies across spatio-temporal scales is required. Thereby, domain-specific languages can play a central role. We are going to a) execute simulation studies to analyse membrane related dynamics, intra-, and intercellular dynamics, b) explore, refine and apply domain-specific languages for modelling at different spatio-temporal scales, for specifying, executing, and documenting simulation experiments, and for checking spatio-temporal properties, and c) support the interactive process of model design and validation beyond individual simulation studies via artefact-based workflows.

Cooperation projects

A02 / A03 / A06 / C01 / C04

Conference papers

Max Schröder, Hendrikje Raben, Frank Krüger, Andreas Ruscheinski, Ursula van Rienen, Adelinde Uhrmacher, Sascha Spors: PROVenance Patterns in Numerical Modelling and Finite Element Simulation Processes of Bio-electric Systems. 41st International Engineering in Medicine and Biology Conference (EMBC), July 2019, Berlin, Germany.

Kai Budde, Julius Zimmermann, Elisa Neuhaus, Max Schröder, Adelinde M. Uhrmacher and Ursula van Rienen: Requirements for Documenting Electrical Cell Stimulation Experiments for Replicability and Numerical Modeling. In: 41st Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC), July 2019, Berlin, Germany.

Andreas Ruscheinski, Kai Budde, Tom Warnke, Pia Wilsdorf, Bjarne Christian Hiller, Marcus Dombrowsky and Adelinde M. Uhrmacher: Generating Simulation Experiments Based on Model Documentations and Templates. In: Winter Simulation Conference (WSC 2018), December 2018, Gothenburg, Sweden. (In Press)

Tom Warnke, Adelinde M. Uhrmacher: Complex simulation experiments made easy. In: Winter Simulation Conference (WSC 2018), December 2018, Gothenburg, Sweden. (In Press)

Tom Warnke, Frank Krüger and Adelinde M. Uhrmacher: Open Simulation Software - Development and Application. In: ASIM 2018 - 24. Symposium Simulationstechnik, October 2018, Hamburg, Germany.

Andreas Ruscheinski, Dragana Gjorgevikj, Marcus Dombrowsky, Kai Budde and  Adelinde M. Uhrmacher: Towards a PROV Ontology for Simulation Models. In: Provenance and Annotation of Data and Processes. Proceedings, published by Springer International Publishing, pp. 192-195, July 2018, London, United Kingdom.

Talks

Adelinde M. Uhrmacher: Multi-Level Modeling and Simulation in Space. Invited Talk, Centro di Ricerca Matematica Ennio De Giorgi, October 2018, Pisa, Italy.

Posters

Kai Budde, Jacob Smith, Andreas Ruscheinski and Adelinde M. Uhrmacher: WebProv: A web-based tool to access, store, and display provenance information of simulation models. In: 10th COMBINE Meeting, July 2019, Heidelberg, Germany.

Kai Budde, Tobias Helms, Fiete Haack and Adelinde M. Uhrmacher: Modeling long-range Wnt signaling with the domain-specific language ML-Rules. In: Workshop for multiscale modeling and simulation to bridge molecular and cellular scales, October 2018, Pisa, Italy.

Philipp Henning, Till Köster and Adelinde M. Uhrmacher: Challenges in reproducing an ODE vesicle transport model with particles in continuous space. In: Workshop for multiscale modeling and simulation to bridge molecular and cellular scales, October 2018, Pisa, Italy.

Kai Budde, Elisa Krummrich, Andreas Ruscheinski, Pia Wilsdorf, Fiete Haack and Adelinde M. Uhrmacher: The Story Behind Wnt Simulation Models: Interrelating Wnt Models by Provenance Information. In: European Wnt Meeting 2018, September 2018, Heidelberg, Germany.

Kai Budde, and Tom Warnke, Adelinde M. Uhrmacher, Eric Schätz, Jens Starke and Fiete Haack: Exploiting equation-free analysis for multi-level, agent-based models in cell biology. In: Winter Simulation Conference (WSC 2017). Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 4564-4565. December 2017, Las Vegas, NV, USA. 

Philipp Henning, Till Köster and Adelinde M. Uhrmacher: Idiosyncracies in Multi-Spatial Modeling. In: 15th Conference on Computational Methods in Systems Biology (CMSB 2017), September 2017, Darmstadt, Germany.

Project leader

Prof. Dr. rer. nat. habil. Adelinde Uhrmacher
E-Mail
Tel.: +49 381 498 7610

Institution

University of Rostock
Institute of Computer Science
Albert-Einstein-Str. 22
18059 Rostock

Associated staff

Philipp Henning
Tom Warnke

Fellowship holders

Philipp Henning (finished)

External website

Domain-specific languages