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

2020

Haack, Fiete; Budde, Kai; Uhrmacher, Adelinde M. (2020): Exploring mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling. In: Journal of cell science. DOI: 10.1242/jcs.243675 .

Stählke, Susanne; Haack, Fiete; Waldner, Anna-Christin; Koczan, Dirk; Moerke, Caroline; Müller, Petra et al. (2020): ROS Dependent Wnt/β-Catenin Pathway and Its Regulation on Defined Micro-Pillars—A Combined In Vitro and In Silico Study. In: Cells 9 (8), S. 1784. DOI: 10.3390/cells9081784 .
 

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.

Conference papers

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 IEEE Engineering in Medicine and Biology Society (EMBC). 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 Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC). Berlin, Germany, July 2019. DOI: 10.1109/EMBC.2019.8856841.

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

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