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

Publications

2019

Köster, Till; Henning, Philipp; Uhrmacher, Adelinde M. (2019): Potential based, spatial simulation of dynamically nested particles. In: BMC bioinformatics 20 (1), S. 607. DOI: 10.1186/s12859-019-3092-y.
 

2018

Winter, Fiete, Wierstorf, Hagen; Hold, Christoph; Kruger, Frank; Raake, Alexander; Spors, Sascha (2018): Colouration in Local Wave Field Synthesis. In: Transactions on Audio, Speech, and Language Processing 26 (10), S. 1913–1924. DOI: 10.1109/TASLP.2018.2842435.

Conference papers

2019

Budde, Kai (2019): Reusing provenance information captured in WebProv for automatic generation of experiment specifications. INtegrative COllaborative modeling in systems MEdicine. Berlin, Germany, November 2019.

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

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

Wilsdorf, Pia; Haack, Fiete, Budde, Kai; Ruscheinski, Andreas; Uhrmacher, Adelinde M. (2019): Conducting Systematic, Partly Automated Simualtion Studies – Unde Venis et Quo Vadis. AIP Conference Proceedings. International Conference on Numerical Analysis and Applied Mathematics. Rhodes, Greece, September 2019.

Wilsdorf, Pia; Zimmermann, Julius; Dombrowsky, Marcus; van Rienen, Ursula; Uhrmacher, Adelinde M. (2019): Simulation Experiment Schemas – Beyond Tools and Simulation Approaches. Winter Simulation Conference. National Harbor, United States of America, December 2019.
 

2018

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

Ruscheinski, Andreas; Gjorgevikj, Dragana; Dombrowsky, Marcus, Budde; Kai, Uhrmacher, Adelinde M. (2018): Towards a PROV Ontology for Simulation Models. In: Provenance and Annotation of Data and Processes. London, United Kingdom, July 2018.

Warnke, Tom; Krüger, Frank; Uhrmacher, Adelinde M. (2018): Open Simulation Software - Development and Application. 24. Symposium Simulationstechnik der Arbeitsgemeinschaft Simulation. Hamburg, Germany, October 2018.

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

Talks

2018

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

Posters

2019

Budde, Kai; Smith, Jacob; Ruscheinski, Andreas; Uhrmacher, Adelinde M. (2019): WebProv: A web-based tool to access, store, and display provenance information of simulation models. 10th COmputational Modeling in BIology NEtwork Meeting. Heidelberg, Germany.
 

2018

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

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

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

2017

Budde, Kai; Warnke, Tom; Uhrmacher, Adelinde M.; Schatz, Eric; Starke, Jens; Haack, Fiete (2017): Exploiting equation-free analysis for multi-level, agent-based models in cell biology. Winter Simulation Conference. Las Vegas, United States of America.

Henning, Philipp; Köster, Till; Uhrmacher, Adelinde M. (2017): Idiosyncracies in Multi-Spatial Modeling. 15th Conference on Computational Methods in Systems Biology. 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