Publications
This is a list of articles that were published in conference proceedings and scientific journals as well as posters and talks at conferences.
List of my publications at my work site
Journal articles
- Danhua Peng, Tom Warnke, and Adelinde M. Uhrmacher (2015): Domain-Specific Languages for Flexbily Experimenting with Stochastic Models. Simulation Notes Europe, 25(2)
[DOI] - Danhua Peng, Tom Warnke, Fiete Haack, and Adelinde M. Uhrmacher (2016): Reusing simulation experiment specifications to support developing models by successive extension. Simulation Modelling Practice and Theory, pp. 68:33–53
[DOI] - Danhua Peng, Tom Warnke, Fiete Haack, and Adelinde M. Uhrmacher (2017): Reusing simulation experiment specifications in developing models by successive composition — a case study of the Wnt/β-catenin signaling pathway. SIMULATION 93(8), pp. 659-677
[DOI] - Tobias Helms, Tom Warnke, Carsten Maus, and Adelinde M. Uhrmacher (2017): Semantics and Efficient Simulation Algorithms of an Expressive Multi-Level Modeling Language. ACM Transactions on Modeling and Computer Simulation 27(2), 8:1-8:25
[DOI] [PDF (ACM DL)] - Tom Warnke, Oliver Reinhardt, Anna Klabunde, Frans Willekens, and Adelinde M. Uhrmacher (2017): Modelling and Simulating Decision Processes of Linked Lives - An Approach Based on Concurrent Processes and Stochastic Race. Population Studies, 71 (sup1), pp. 69-83
[DOI] - Maria E. Pierce, Tom Warnke, Uwe Krumme, Tobias Helms, Cornelius Hammer, and Adelinde M. Uhrmacher (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
[DOI] - Oliver Reinhardt, Jason D. Hilton, Tom Warnke, Jakub Bijak, Adelinde M. Uhrmacher (2018): Streamlining simulation experiments with agent-based models in demography. Journal of Artificial Societies and Social Simulation, 21 (3)
[DOI] - Tom Warnke, Tobias Helms, and Adelinde M. Uhrmacher (2018): Reproducible and flexible simulation experiments with ML-Rules and SESSL. Bioinformatics, 34 (8), pp. 1424-1427
[DOI] - Andreas Ruscheinski, Tom Warnke, and Adelinde M. Uhrmacher (2019): Artifact-based Workflows for Supporting Simulation Studies. IEEE Transactions on Knowledge and Data Engineering
[DOI]
Conference articles
- Tom Warnke, Tobias Helms, and Adelinde M. Uhrmacher (2015): Syntax and Semantics of a Multi-Level Modeling Language. In Proceedings of the 3rd ACM Conference on SIGSIM-Principles of Advanced Discrete Simulation, London, United Kingdom, June 10-12, 2015, pp. 133–144
[DOI] [PDF (ACM DL)] - Tom Warnke, Alexander Steiniger, Adelinde M. Uhrmacher, Anna Klabunde, and Frans Willekens (2015): ML3: a language for compact modeling of linked lives in computational demography.. Proceedings of the 2015 Winter Simulation Conference, Huntington Beach, CA, USA, December 6-9, 2015, pp. 2764–2775
[DOI] - Tom Warnke and Adelinde M. Uhrmacher (2016): Spatiotemporal Pattern Matching in RoboCup. In Matthias Klusch, Rainer Unland, Onn Shehory, Alexander Pokahr, and Sebastian Ahrndt, editors, MATES, volume 9872 of Lecture Notes in Computer Science, pp. 89–104.
Best Paper Award Nominee
[DOI] [Presentation slides (PDF)] - Tom Warnke, Oliver Reinhardt, and Adelinde M. Uhrmacher (2016): Population-based CTMCs and Agent-based Models. In Proceedings of the Winter Simulation Conference 2016
Received ACM SIGSIM Best Ph.D. Student Paper Award
[DOI] [Presentation slides (PDF)] - Tom Warnke, Frank Krüger, and Adelinde M. Uhrmacher (2017): Open Simulation Software - Development and Application. ASIM 2018 - 24. Symposium Simulationstechnik, 4-5 Oct 2018, Hamburg, Germany
[PDF] [Presentation slides (PDF)] - Andreas Ruscheinski, Kai Budde, Tom Warnke, Pia Wilsdorf, Bjarne C. Hiller, Marcus Dombrowsky, and Adelinde M. Uhrmacher (2018): Generating Simulation Experiments Based on Model Documentations and Templates. Proceedings of the 2018 Winter Simulation Conference, Gothenburg, Sweden, December 9-12, 2018, pp. 715-726
[DOI] - Tom Meyer, Tobias Helms, Tom Warnke, and Adelinde M. Uhrmacher (2018): Runtime code generation for interpreted domain-specific modeling languages. Proceedings of the 2018 Winter Simulation Conference, Gothenburg, Sweden, December 9-12, 2018, pp. 605-615
[DOI] - Tom Warnke and Adelinde M. Uhrmacher (2018): Complex simulation experiments made easy. Proceedings of the 2018 Winter Simulation Conference, Gothenburg, Sweden, December 9-12, 2018, pp. 410-424
[DOI] [Presentation slides (PDF)] - Tom Warnke and Adelinde M. Uhrmacher (2019): Reproducible parallel simulation experiments via pure functional programming. Proceedings of the 2019 DS-RT, Cosenza, Italy, October 7-9, 2019
[DOI] [Presentation slides (PDF)] - Till Köster, Tom Warnke, and Adelinde M. Uhrmacher (2020): Partial evaluation via code generation for static stochastic reaction network models. Proceedings of the 2020 PADS, Miami, Florida, USA, June 15-17, 2020
[DOI] [PDF (ACM DL)] - Andreas Ruscheinski, Anja Wolpers, Philipp Henning, Tom Warnke, Fiete Haack, and Adelinde M. Uhrmacher (2020): Pragmatic Logic-based Spatio-temporal Pattern Checking in Particle-based Models. Proceedings of the 2020 Winter Simulation Conference, Orlando, FL, USA, December 13-16, 2020
[PDF (Open Access)] - Tom Warnke and Adelinde M. Uhrmacher (2021): Nonlinear pattern matching in rule-based modeling languages. Proceedings of the 2021 CMSB, Bordeax, France, September 22-24, 2021
[DOI] [Presentation slides (PDF)] - Justin N. Kreikemeyer, Till Köster, Adelinde M. Uhrmacher, and Tom Warnke (2021): Inferring Dependency Graphs for Agent-based Models Using Aspect-oriented Programming. Proceedings of the 2021 Winter Simulation Conference, Phoenix, AZ, USA, December 13-17, 2021
In Press
Chapters in books
- Tobias Helms, Tom Warnke, and Adelinde M. Uhrmacher (2019): Multi-Level Modeling and Simulation of Cellular Systems: An Introduction to ML-Rules. Hlavacek W. (eds) Modeling Biomolecular Site Dynamics. Methods in Molecular Biology, vol 1945. Humana Press, New York, NY, pp 141-160
[DOI] - Oliver Reinhardt, Tom Warnke, Andreas Ruscheinski, and Adelinde M. Uhrmacher (2019): Valid and Reproducible Simulation Studies - Making It Explicit. Beisbart C., Saam N. (eds) Computer Simulation Validation. Simulation Foundations, Methods and Applications. Springer, Cham, pp 607-627
[DOI]
Posters and short papers
- Tom Warnke, Adelinde M. Uhrmacher (2014): An Approach for Spatial Pattern Matching in Simulation Trajectories. In Proceedings of the 2014 Winter Simulation Conference, Savannah, Georgia, USA, December 7-10, 2014, pages 4039–4040
[Abstract (PDF)] [Poster (PDF)] - Maria E. Pierce, Tom Warnke, Tobias Helms, Adelinde M. Uhrmacher, Uwe Krumme, and Cornelius Hammer (2015): Individual-based cod simulation with ML-Rules. In Proceedings of the 2015 Winter Simulation Conference, Huntington Beach, CA, USA, December 6-9, 2015, pages 3192–3193
[DOI] - Tom Warnke (2016): A DSL for Continuous-Time Agent-Based Modeling and Simulation. In Proceedings of the Winter Simulation Conference 2016
[DOI] [Poster (PDF)] [Presentation slides (PDF)] - Tom Warnke, Lars Roesicke, Hans-Jörg Schulz, and Adelinde M. Uhrmacher (2017): Simulation Galleries - Combining Experiment Design and Visual Analytics. INFORMS Simulation Society 2017 Research Workshop
- Tom Warnke and Adelinde M. Uhrmacher (2017): Practical expressiveness of internal and external domain-specific modeling languages. In Proceedings of the Winter Simulation Conference 2017
[DOI] - Kai Budde, Tom Warnke, Adelinde M. Uhrmacher, Eric Schätz, Jens Starke, and Fiete Haack (2017): Exploiting equation-free analysis for multi-level, agent-based models in cell biology. In Proceedings of the Winter Simulation Conference 2017
[DOI] - Tom Warnke and Adelinde M. Uhrmacher (2020): Simulation projects with Computer Science undergraduate students. Proceedings of the 2020 Winter Simulation Conference, Orlando, FL, USA, December 13-16, 2020
[PDF (Open Access)] [Poster (PDF)]