Publications

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2008
Ewald R, Himmelspach J, Uhrmacher A.  2008.  An Algorithm Selection Approach for Simulation Systems. Proc. ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation PADS'08.
2010
Ewald R, Himmelspach J, Jeschke M, Leye S, Uhrmacher A.  2010.  Flexible Experimentation in the Modeling and Simulation Framework JAMES II - Implications for Computational Systems Biology. Briefings in Bioinformatics. 11:290-300.
2011
Jeschke M, Ewald R, Uhrmacher A.  2011.  Exploring the Performance of Spatial Stochastic Simulation Algorithms. Journal of Computational Physics.
Schulz H-J, Uhrmacher A, Schumann H.  2011.  Visual Analytics for Stochastic Simulation in Cell Biology. Proceedings of the International Conference on Knowledge Management and Knowledge Technologies (iKNOW'11).
2012
Helms T, Rybacki S, Ewald R, Uhrmacher A.  2012.  An adaptive simulator for ML-rules. :Poster@WinterSimulationConference(WSC'12).
John M, Schulz H-J, Schumann H, Uhrmacher A, Unger A.  2012.  Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models. to appear in Formal Aspects of Computing.
Luboschik M, Maus C, Schulz H-J, Schumann H, Uhrmacher A.  2012.  Heterogeneity-based guidance for exploring multiscale data in Systems Biology. Proceedings of the IEEE Symposium on Biological Data Visualization (BioVis'12).
Luboschik M, Maus C, Schulz H-J, Schumann H, Uhrmacher A.  2012.  Heterogeneity-based Guidance for Exploring Multiscale Data in Systems Biology.
Luboschik M, Rybacki S, Ewald R, Schwarze B, Schumann H, Uhrmacher A.  2012.  Interactive Visual Exploration of Simulator Accuracy: A Case Study for Stochastic Simulation Algorithms. Proceedings of the Winter Simulation Conference (WSC'2012).
Schützel J, Himmelspach J, Meyer H, Heuer A, Uhrmacher A.  2012.  Streaming data management for the online processing of simulation data. :Poster@WinterSimulationConference(WSC'12).
Rybacki S, Leye S, Himmelspach J, Uhrmacher A.  2012.  Template and Frame based Experiment Workflows in Modeling and Simulation Software with WORMS. Seventh IEEE 2012 World Congress on Services - Sixth International Workshop on Scientific and Engineering Workflows: Advances in Data and Event-Driven Workflows.
Helms T, Himmelspach J, Maus C, Röwer O, Schützel J, Uhrmacher A.  2012.  Toward a language for the flexible observation of simulations. Proc. of the Winter Simulation Conference (WSC'12).
Luboschik M, Tominski C, Bittig AT, Uhrmacher A, Schumann H.  2012.  Towards Interactive Visual Analysis of Microscopic-Level Simulation Data. Proceedings of the Annual SIGRAD Conference, Special Theme: Interactive Visual Analysis of Data.
Rybacki S, Himmelspach J, Uhrmacher A.  2012.  Using workflows to control the experiment execution in M&S Software. Proceedings of the 5th SimuTools conference.
2013
Helms T, Luboschik M, Schumann H, Uhrmacher A.  2013.  An Approximate Execution of Rule-Based Multi-level Models. Computational Methods in Systems Biology. 8130:19--32.
John M, Schulz H-J, Schumann H, Uhrmacher A, Unger A.  2013.  Constructing and Visualizing Chemical Reaction Networks from Pi-Calculus Models. Formal Aspects of Computing. 25(5):723--742.
Helms T, Ewald R, Rybacki S, Uhrmacher A.  2013.  A Generic Adaptive Simulation Algorithm for Component-based Simulation Systems. Proceedings of the 2013 ACM SIGSIM conference on Principles of advanced discrete simulation.
Haack F, Burrage K, Redmer R, Uhrmacher A.  2013.  Studying the Role of Lipid Rafts on Protein Receptor Bindings with Cellular Automata. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS. 10(3)
2014
Rybacki S, Haack F, Wolf K, Uhrmacher A.  2014.  Developing simulation models - from conceptual to executable model and back - an artifact-based workflow approach. Simutools.
Helms T, Ewald R, Rybacki S, Uhrmacher A.  2014.  A Generic Adaptive Simulation Algorithm for Component-based Simulation Systems. ACM Transactions on Modeling and Computer Simulation. 1(2)
Schützel J, Meyer H, Uhrmacher A.  2014.  A Stream-Based Architecture for the Management and On-Line Analysis of Unbounded Amounts of Simulation Data. SIGSIM-PADS '14.
2015
Kossow C, Rybacki S, Millat T, Rateitschak K, Jaster R, Uhrmacher A, Wolkenhauer O.  2015.  An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers. Mathematical and Computer Modelling of Dynamical Systems. 21(6)