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Wilsdorf, Pia and Heller, Jakob and Budde, Kai and Zimmermann, Julius and Warnke, Tom and Haubelt, Christian and Timmermann, Dirk and van Rienen, Ursula and Uhrmacher, Adelinde M. (2022) A Model-Driven Approach for Conducting Simulation Experiments. Applied Sciences, 12 (16), ISSN 2076-3417.
Budde, Kai and Smith, Jacob and Wilsdorf, Pia and Haack, Fiete and Uhrmacher, Adelinde M. (2021) Relating simulation studies by provenance—Developing a family of Wnt signaling models. PLoS Computational Biology, 17 (8), pp. 1-21. ISSN 1553-7358 (print) 1553-734X (online).
Zimmermann, Julius and Budde, Kai and Arbeiter, Nils and Molina, Francia and Storch, Alexander and Uhrmacher, Adelinde M. and van Rienen, Ursula (2021) Using a digital twin of an electrical stimulation device to monitor and control the electrical stimulation of cells in vitro. Frontiers in Bioengineering and Biotechnology, 9, ISSN 2296-4185.
Haack, Fiete and Budde, Kai and Uhrmacher, Adelinde M. (2020) Exploring mechanistic and temporal regulation of LRP6 endocytosis in canonical WNT signaling. Journal of Cell Science, 133 (15), ISSN 0021-9533.
Budde, Kai and Neuhaus, Elisa and Molina, Francia and Zimmermann, Julius and Arbeiter, Nils and Storch, Alexander and van Rienen, Ursula and Uhrmacher, Adelinde M. (2020) Documenting an Electrical Cell Stimulation Experiment–Guidelines at Work. In: Conference on Progress in Electrically Active Implants Tissue and Functional Regeneration (ELAINE 2020), 29-30 Sep 2020, Virtual. Proceedings,, Rostock, Germany, p. 21.
Budde, Kai and Zimmermann, Julius and Neuhaus, Elisa and Schröder, Max and Uhrmacher, Adelinde M. and van Rienen, Ursula (2019) 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), 23-27 July 2019, Berlin, Germany. Proceedings, published by IEEE, pp. 1082-1088.
Budde, Kai and Smith, Jacob and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) WebProv: A web-based tool to access, store, and display provenance information of simulation models. In: 10th "Computational Modeling in Biology Network" (COMBINE) Meeting, 15-19 Jul 2019, Heidelberg, Germany. Poster.
Wilsdorf, Pia and Haack, Fiete and Budde, Kai and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) Conducting Systematic, Partly Automated Simulation Studies – Unde Venis et Quo Vadis. In: 17th International Conference of Numerical Analysis and Applied Mathematics, 23-28 Sep 2019, Rhodes, Greece. Proceedings, published by AIP Publishing LCC, AIP Conference Proceedings 2293(1), 020001.
Budde, Kai and Wilsdorf, Pia and Smith, Jacob and Haack, Fiete and Ruscheinski, Andreas and Uhrmacher, Adelinde M. (2019) Reusing provenance information captured in WebProv for automatic generation of experiment specifications. In: INCOME 2019 (Integrative pathway modeling in systems biology and systems medicine), 25-29 Nov 2019, Berlin, Germany.
Budde, Kai and Helms, Tobias and Haack, Fiete and Uhrmacher, Adelinde M. (2018) Modeling long-range Wnt signaling with the domain-specific language ML-Rules. In: Workshop on "Multiscale modeling and simulations to bridge molecular and cellular scales" of the Centro di Ricerca Matematica Ennio De Giorgi, 1-5 Oct 2018, Pisa, Italy. Poster.
Ruscheinski, Andreas and Budde, Kai and Warnke, Tom and Wilsdorf, Pia and Hiller, Bjarne Christian and Dombrowsky, Marcus and Uhrmacher, Adelinde M. (2018) Generating Simulation Experiments Based on Model Documentations and Templates. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Proceedings, published by IEEE, pp. 715-726.
Budde, Kai and Krummrich, Elisa and Ruscheinski, Andreas and Wilsdorf, Pia and Haack, Fiete and Uhrmacher, Adelinde M. (2018) The Story Behind Wnt Simulation Models: Interrelating Wnt Models by Provenance Information. In: European Wnt Meeting 2018, 12-14 Sep 2018, Heidelberg. Poster.
Ruscheinski, Andreas and Gjorgevikj, Dragana and Dombrowsky, Marcus and Budde, Kai and Uhrmacher, Adelinde M. (2018) Towards a PROV Ontology for Simulation Models. In: Provenance and Annotation of Data and Processes, 09-10 Jul 2018, London, UK. Proceedings, published by Springer International Publishing, pp. 192-195.
Budde, Kai and Warnke, Tom and Uhrmacher, Adelinde M. and Schätz, Eric and Starke, Jens and Haack, Fiete (2017) Exploiting equation-free analysis for multi-level, agent-based models in cell biology. In: Winter Simulation Conference (WSC 2017), 3-6 Dec 2017, Las Vegas, NV, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 4564-4565. Poster.
