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Henning, Philipp and Köster, Till and Haack, Fiete and Burrage, Kevin and Uhrmacher, Adelinde M. (2023) Implications of different membrane compartmentalization models in particle-based in silico studies. Royal Society Open Science, 10 (7), e221177. ISSN 2054-5703.
Köster, Till and Warnke, Tom and Uhrmacher, Adelinde M. (2022) Generating Fast Specialized Simulators for Stochastic Reaction Networks via Partial Evaluation. ACM Transactions on Modeling and Computer Simulation (TOMACS), 32 (2), pp. 1-25. ISSN 1049-3301 (print) 1558-1195 (online).
Haack, Fiete and Köster, Till and Uhrmacher, Adelinde M. (2021) Receptor/raft ratio is a determinant for LRP6 phosphorylation and WNT/β-catenin signaling. Frontiers in Cell and Developmental Biology, 9, p. 2085. ISSN 2296-634X.
Foguelman, Daniel and Henning, Philipp and Uhrmacher, Adelinde M. and Castro, Rodrigo (2021) EB-DEVS: A formal framework for modeling and simulation of emergent behavior in dynamic complex systems. Journal of Computational Science, 53, p. 101387. ISSN 18777503.
Köster, Till and Henning, Philipp and Uhrmacher, Adelinde M. (2019) Potential based, spatial simulation of dynamically nested particles. BMC Bioinformatics, 20 (607), ISSN 1471-2105.
Warnke, Tom and Helms, Tobias and Uhrmacher, Adelinde M. (2018) Reproducible and flexible simulation experiments with ML-Rules and SESSL. Bioinformatics, 34 (8), pp. 1424-1427. ISSN 1367-4803.
Pierce, Maria E. and Warnke, Tom and Krumme, Uwe and Helms, Tobias and Hammer, Cornelius and Uhrmacher, Adelinde M. (2017) Developing and validating a multi-level ecological model of eastern Baltic cod (Gadus morhua) in the Bornholm Basin - a case for domain-specific languages. Ecological Modeling, 361, pp. 49-65. ISSN 0304-3800.
Helms, Tobias and Warnke, Tom and Maus, Carsten and Uhrmacher, Adelinde M. (2017) Semantics and Efficient Simulation Algorithms of an Expressive Multi-Level Modeling Language. ACM Transactions on Modeling and Computer Simulation (TOMACS), 27 (2), 8:1-8:25. ISSN 1049-3301 (print) 1558-1195 (online).
Helms, Tobias and Mentel, Steffen and Uhrmacher, Adelinde M. (2016) Dynamic State Space Partitioning for Adaptive Simulation Algorithms. EAI Endorsed Transactions on Collaborative Computing, 16 (10), e2. ISSN 2312-8623.
Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M. (2015) Automatic Runtime Adaptation for Component-Based Simulation Algorithms. ACM Transactions on Modeling and Computer Simulation (TOMACS), 26 (1), 7:1-7:24. ISSN 1049-3301 (print) 1558-1195 (online).
Haack, Fiete and Lemcke, Heiko and Ewald, Roland and Rharass, Tareck and Uhrmacher, Adelinde M. (2015) Spatio-temporal Model of Endogenous ROS and Raft-Dependent WNT/Beta-Catenin Signaling Driving Cell Fate Commitment in Human Neural Progenitor Cells. PLoS Computational Biology, 11 (3), e104106. ISSN 1553-7358 (print) 1553-734X (online).
Helms, Tobias and Warnke, Tom and Uhrmacher, Adelinde M. (2019) Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules. In: Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, 1945 . Humana Press, New York, NY, pp. 141-160. ISBN 978-1-4939-9100-6 (print) 978-1-439-9102-0 (Online).
Andelfinger, Philipp and Köster, Till and Uhrmacher, Adelinde M. (2023) Zero Lookahead? Zero Problem. The Window Racer Algorithm. In: SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2023), 21-23 Jun 2023, Orlando, Florida, USA. Proceedings, published by Association for Computing Machinery (ACM), New York, NY, USA, pp. 1-11.
Köster, Till and Herrmann, Leon and Andelfinger, Philipp and Uhrmacher, Adelinde M. (2022) GPU-Accelerated Simulation Ensembles of Stochastic Reaction Networks. In: Winter Simulation Conference (WSC 2022), 11-14 Dec 2022, Singapore. Proceedings, published by IEEE, pp. 2570-2581.
Köster, Till and Uhrmacher, Adelinde M. and Andelfinger, Philipp (2022) Towards an Open Repository for Reproducible Performance Comparison of Parallel and Distributed Discrete-Event Simulators. In: ACM Conference SIGSIM Principles of Advanced Discrete Simulation (PADS 2022), 08-10 Jun 2022, Atlanta, GA, USA (Virtuell). Proceedings, published by ACM, New York, NY, USA, pp. 31-32.
Warnke, Tom and Uhrmacher, Adelinde M. (2021) Nonlinear pattern matching in rule-based modeling languages. In: 19th International Conference on Computational Methods in Systems Biology (CMSB 2021), 22-24 Sep 2021, Bordeaux, France. Proceedings, published by Springer International Publishing, Cham, pp. 198-214.
Kreikemeyer, Justin N. and Hillston, Jane and Uhrmacher, Adelinde M. (2020) Probing the Performance of the Edinburgh Bike Sharing System using SSTL. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2020), 15-17 Jun 2020, Miami, Florida, USA. Proceedings, published by ACM, New York, USA, pp. 141-152.
Köster, Till and Giabbanelli, Philippe J. and Uhrmacher, Adelinde M. (2020) Performance and Soundness of Simulation: A Case Study based on a Cellular Automaton for In-Body Spread of HIV. In: Winter Simulation Conference (WSC 2020), 13-16 Dec 2020, Orlando, Florida, USA. Proceedings, published by IEEE Computer Society, pp. 2281-2292.
Köster, Till and Warnke, Tom and Uhrmacher, Adelinde M. (2020) Partial evaluation via code generation for static stochastic reaction network models. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2020), 15-17 Jun 2020, Miami, Florida, USA. Proceedings, published by ACM, New York, USA, pp. 159-170.
Wilsdorf, Pia and Pierce, Maria E. and Hillston, Jane and Uhrmacher, Adelinde M. (2019) Round-based Super-Individuals - Balancing Speed and Accuracy. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2019), 03-05 Jun 2019, Chicago, IL, USA. Proceedings, published by ACM, New York, USA, pp. 95-98.
Köster, Till and Drüeke, Nicola M. and Uhrmacher, Adelinde M. (2018) Latency Optimized Execution of Sequential Simulators by Parallel Parameter Optimization. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Poster.
Köster, Till and Hauptmann, Felix and Uhrmacher, Adelinde M. (2018) Optimizing Data Structures for Highly Dynamic Content in Collective, Adaptive Systems. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Poster.
Helms, Tobias and Wilsdorf, Pia and Uhrmacher, Adelinde M. (2018) Hybrid Simulation of Dynamic Reaction Networks in Multi-Level Models. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2018), 23-25 May 2018, Rome, Italy. Proceedings, published by ACM, New York, NY, USA, pp. 133-144.
Köster, Till and Uhrmacher, Adelinde M. (2018) Handling Dynamic Sets of Reactions in Stochastic Simulation Algorithms. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2018), 23-25 May 2018, Rome, Italy. Proceedings, published by ACM, New York, NY, USA, pp. 161-164.
Meyer, Tom and Helms, Tobias and Warnke, Tom and Uhrmacher, Adelinde M. (2018) Runtime Code Generation for Interpreted Domain-Specific Modeling Languages. In: Winter Simulation Conference (WSC 2018), 09-12 Dec 2018, Gothenburg, Sweden. Proceedings, published by IEEE, pp. 605-616.
Köster, Till and Uhrmacher, Adelinde M. (2017) Multi-Level Particle-Based Modeling and Simulation of Cell Biological Systems. In: V International Conference on Particle-Based Methods, 26-28 Sep 2017, Hannover, Germany. Invited Talk.
Henning, Philipp and Köster, Till and Uhrmacher, Adelinde M. (2017) Idiosyncracies in Multi-Spatial Modeling. In: 15th Conference on Computational Methods in Systems Biology (CMSB 2017), 27-29 Sep 2017, Darmstadt, Germany. Poster.
Köster, Till and Perumalla, Kalyan and Uhrmacher, Adelinde M. (2017) Efficient Simulation of Nested Hollow Sphere Intersections for Dynamically Nested Compartmental Models in Cell Biology. In: ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2017), 24-26 May 2017, Singapore. Proceedings, published by ACM New York, NY, USA, pp. 173-183.
Helms, Tobias and Mentel, Steffen and Uhrmacher, Adelinde M. (2016) Dynamic State Space Partitioning for Adaptive Simulation Algorithms. In: 9th EAI International Conference on Performance Evaluation Methodologies and Tools, 14-16 Dec 2015, Berlin, Germany. Proceedings, published by ICST, Brussels, Belgium, pp. 149-152.
Kossow, Christina and Helms, Tobias and Kreutzer, Jan M. and Martens, Alke and Uhrmacher, Adelinde M. (2016) Evaluating Different Modeling Languages Based on a User Study. In: 49th Annual Simulation Symposium (ANNS 2016), 3-6 Apr 2016, Pasadena, CA, USA. Proceedings, published by Society for Computer Simulation International, San Diego, CA, USA, 18:1-18:8.
Helms, Tobias and Reinhardt, Oliver and Uhrmacher, Adelinde M. (2015) Bayesian changepoint detection for generic adaptive simulation algorithms. In: 48th Annual Simulation Symposium (ANSS 2015) part of the Spring Simulation Multiconference (SpringSim 2015), 12-15 Apr, Alexandria, VA, USA. Proceedings, published by Society for Computer Simulation International, San Diego, CA, USA, pp. 62-69.
Warnke, Tom and Helms, Tobias and Uhrmacher, Adelinde M. (2015) Syntax and Semantics of a Multi-Level Modeling Language. In: 3rd ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2015), 10-12 Jun 2015, London, UK. Proceedings, published by ACM, New York, NY, USA, pp. 133-144.
Helms, Tobias and Maus, Carsten and Haack, Fiete and Uhrmacher, Adelinde M. (2014) Multi-level modeling and simulation of cell biological systems with ML-rules: a tutorial. In: Winter Simulation Conference (WSC 2014), 7-10 Dec 2014, Savannah, GA, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305 Print ISSN: 0891-7736, pp. 177-191.
Helms, Tobias and Uhrmacher, Adelinde M. (2014) Hybrid Execution of Dynamic Rule-based Multi-level Models. In: Winter Simulation Conference (WSC 2014), 7-10 Dec 2014, Savannah, GA, USA. Poster.
Warnke, Tom and Peng, Danhua and Haack, Fiete and Uhrmacher, Adelinde M. (2014) Towards a Language for Specifying Properties of Simulation Trajectories. In: International Conference on Computational Methods in Systems Biology (CMSB 2014), 17-19 Nov 2014, Manchester, UK. Poster.
Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M. (2013) A generic adaptive simulation algorithm for component-based simulation systems. In: SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS 2013), 19-22 May 2013, Montreal, QC, Canada. Proceedings, published by ACM, NewYork, USA, pp. 11-22.
Helms, Tobias and Luboschik, Martin and Schumann, Heidrun and Uhrmacher, Adelinde M. (2013) An Approximate Execution of Rule-Based Multi-level Models. In: 11th International Conference on Computational Methods in Systems Biology (CMSB 2013), 22-24 Sep 2013, Klosterneuburg, Austria. Proceedings, published by Springer, Berlin, Heidelberg, Lecture Notes in Computer Science (LNCS), volume 8130, pp. 19-32.
Nähring, Sebastian and Ewald, Roland and Uhrmacher, Adelinde M. and Maus, Carsten (2013) From standardized modeling formats to modeling languages and back - An exploration based on SBML and ML-Rules. In: Winter Simulations Conference (WSC 2013), 08-11 Dec 2013, Washington, D.C., USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305 Print ISSN: 0891-7736, pp. 1359-1370.
Herrmann, Leon (2023) Comparing the Performance of Stochastic Simulators Using a Synthetic Benchmark. Masters thesis, Institute for Visual and Analytic Computing, University of Rostock.
Herrmann, Leon (2021) Parallele Simulation von Ensemblen stochastischer Simulationen auf Grafikkarten. Bachelor thesis, Institute for Visual and Analytic Computing, University of Rostock.
Hauptmann, Felix (2020) Erzeugung statischer Reaktionsnetze aus dynamisch geschachtelten Regelsystemen. Masters thesis, Institute for Visual and Analytic Computing, University of Rostock.
Wilsdorf, Pia (2018) Super-Individuals - to Balance Speed and Accuracy of Individual-based Models on Demand. Masters thesis, Institute of Computer Science, University of Rostock.
Büchner, Eric (2018) Entwicklung eines visuellen ML-Rules Editors. Bachelor thesis, Universität Rostock, Institut für Informatik.
Flaegel, Stephan (2018) Die Rejection-based Method für ML-Rules. Bachelor thesis, Universität Rostock, Institut für Informatik.
Helms, Tobias (2017) Simulator Adaption at Runtime for Component-Based Simulation Software. PhD thesis, Institut of Computer Science, University of Rostock.
Ahsan, Sohaib (2017) Parallel and Distributed Simulation of ML-Rules Models. Masters thesis, Institute of Computer Science, University of Rostock.
Köster, Till (2017) Combined particle and compartmental dynamics of cell-biological models using hollow spheres on the GPU. Masters thesis, Institut of Computer Science, University of Rostock.
Haack, Fiete (2016) Exploring the spatio-temporal dynamics of lipid rafts and their role in signal transduction. PhD thesis, Institute of Computer Science, University of Rostock.
Wilsdorf, Pia (2016) Approximation diskreter Ereignisse bei hybrid ausgeführten ML-Rules Simulationen. Bachelor thesis, Institute of Computer Science, University of Rostock.
Mentel, Steffen (2014) Konfiguration dynamischer Zustandsräume für adaptive Simulationsalgorithmen. Bachelor thesis, Institut für Informatik, Universität Rostock.
Nähring, Sebastian (2014) Functions on Solutions - Language Extension of ML-Rules. Masters thesis, Institute of Computer Science, University of Rostock.
Reinhardt, Oliver (2014) Bayessche Changepoint-Detection zur Unterstützung adaptiver Simulationsalgorithmen. Bachelor thesis, Institut für Informatik, Universität Rostock.
Zabel, Jakob (2014) Statistisches Testen von komponenten-basierten stochastischen Simulationsalgorithmen. Masters thesis, Institut für Informatik, Universität Rostock.
Holle, Marcel (2013) Dynamische Zustandsraumrepräsentation für Adaptive Simulationsalgorithmen. Bachelor thesis, Institut für Informatik, Universität Rostock.
Helms, Tobias (2012) Adaptive Laufzeit-Rekonfiguration von ML-Rules Simulationen. Masters thesis, Institut für Informatik, Universität Rostock.
Gilbert, David and Heiner, Monika and Takahashi, Koichi and Uhrmacher, Adelinde M. (2015) Multiscale Spatial Computational Systems Biology (Dagstuhl Seminar 14481). Schloss Dagstuhl--Leibniz-Zentrum für Informatik, Dagstuhl, Germany.
