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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).
John, Mathias and Schulz, Hans-Jörg and Schumann, Heidrun and Uhrmacher, Adelinde M. and Unger, Andrea (2013) Constructing and visualizing chemical reaction networks from pi-calculus models. Formal Aspects of Computing, 25 (5), pp. 723-742. ISSN 0934-5043.
Luboschik, Martin and Tominski, Christian and Bittig, Arne T. and Uhrmacher, Adelinde M. and Schumann, Heidrun (2012) Towards Interactive Visual Analysis of Microscopic-Level Simulation Data. In: Interactive Visual Analysis of Data (SIGRAD 2012), 29-30 Nov 2012, Växjö, Sweden. Proceedings, published by Linköping University Electronic Press, Linköpings universitet, Sweden, pp. 91-94.
Maus, Carsten and Rybacki, Stefan and Uhrmacher, Adelinde M. (2011) Rule-based multi-level modeling of cell biological systems. BMC Systems Biology, 5 (166), ISSN 1752-0509 (electronic version).
Mazemondet, Orianne and Hübner, Rayk and Frahm, Jana and Koczan, Dirk and Bader, Benjamin and Weiss, Dieter and Uhrmacher, Adelinde M. and Frech, Moritz and Rolfs, Arndt and Luo, Jiankai (2011) Quantitative and kinetic profile of Wnt/β-catenin signaling components during human neural progenitor cell differentiation. Cellular and Molecular Biology Letters, 16 (4), pp. 515-538. ISSN 1689-1392.
Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M. (2011) Exploring the performance of spatial stochastic simulation algorithms. Journal of Computational Physics, 230 (7), pp. 2562-2574. ISSN 0021-9991.
Bittig, Arne T. and Haack, Fiete and Maus, Carsten and Uhrmacher, Adelinde M. (2011) Adapting rule-based model descriptions for simulating in continuous and hybrid space. In: 9th International Conference on Computational Methods in Systems Biology (CMSB 2011), 21-23 Sep 2011, Paris, France. Proceedings, published by ACM, NewYork, USA, pp. 161-170.
Maus, Carsten and Rybacki, Stefan and Uhrmacher, Adelinde M. (2011) Formal Rule-based Multi-Level Modeling. In: 12th International Conference on Systems Biology (ICSB 2011), 28 Aug - 01 Sep, Heidelberg - Mannheim, Germany. Poster.
Mazemondet, Orianne (2011) Spatio-temporal Dynamics of the Wnt/ß-catenin Signaling Pathway: A Computational Systems Biology Approach. PhD thesis, Institute of Computer Science, University of Rostock.
Schulz, Hans-Jörg and Uhrmacher, Adelinde M. and Schumann, Heidrun (2011) Visual analytics for stochastic simulation in cell biology. In: 11th International Conference on Knowledge Management and Knowledge Technologies (i-KNOW 2011), 07-09 Sep 2011, Graz, Austria. Proceedings, published by ACM, NewYork, USA, 48:1-48:8.
Bittig, Arne T. and Jeschke, Matthias and Uhrmacher, Adelinde M. (2010) Towards Modelling and Simulation of Crowded Environments in Cell Biology. In: International Conference of Numerical Analysis and Applied Mathematics (ICNAAM 2010), 19-25 Sep 2010, Rhodes, Greece. Proceedings, published by AIP Conference Proceedings, 1281(1), pp. 1326-1329.
Bittig, Arne T. and Uhrmacher, Adelinde M. (2010) Spatial modeling in cell biology at multiple levels. In: Winter Simulation Conference (WSC 2010), 05-08 Dec 2010, Baltimore, Maryland, USA. Proceedings, published by IEE, Electronic ISSN: 1558-4305, pp. 608-619.
Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M. (2010) Flexible experimentation in the modeling and simulation framework JAMES II - implications for computational systems biology. Briefings in Bioinformatics, 11 (3), pp. 290-300. ISSN 1467-5463.
Ewald, Roland and Schulz, Rene and Uhrmacher, Adelinde M. (2010) Selecting Simulation Algorithm Portfolios by Genetic Algorithms. In: 24th ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS 2010), 17-19 May 2010, Atlanta, Georgia, USA. Proceedings, published by IEEE, Print ISSN: 1087-4097, pp. 48-56.
Haack, Fiete and Leye, Stefan and Uhrmacher, Adelinde M. (2010) A flexible architecture for modeling and simulation of diffusional association. In: 3rd Workshop From Biology To Concurrency and back, FBTC 2010, 27 Mar 2010, Paphos, Cyprus. Proceedings, published by Electronic Proceedings in Theoretical Computer Science (EPTCS), 19, pp. 70-84.
Himmelspach, Jan and Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M. (2010) Enhancing the Scalability of Simulations by Embracing Multiple Levels of Parallelization. In: Second International Workshop on High Performance Computational Systems Biology, 30 Sep - 01 Oct 2010, Twente, The Netherlands. Proceedings, published by IEEE, pp. 57-66.
Himmelspach, Jan and Röhl, Mathias and Uhrmacher, Adelinde M. (2010) Component-Based Models and Simulations for Supporting Valid Multi-Agent System Simulations. Applied Artificial Intelligence, 24 (5), pp. 414-442. ISSN 0883-9514 (print) 1087-6545 (online).
John, Mathias (2010) Reaction Constraints for the Pi-Calculus - A Language for the Stochastic and Spatial Modeling of Cell-Biological Processes. PhD thesis, Institute of Computer Science, University of Rostock.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim and Uhrmacher, Adelinde M. (2010) The Attributed Pi-Calculus with Priorities. Transactions on Computational Systems Biology 12, pp. 13-76.
Leye, Stefan and John, Mathias and Uhrmacher, Adelinde M. (2010) A flexible architecture for performance experiments with the pi-Calculus and its extensions. In: 3rd International Conference on Simulation Tools and Techniques (SIMUTOOLS 2010), 15-19 Mar 2010, Torremolinos, Malaga, Spain. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, 35:1-35:10.
Leye, Stefan and Mazemondet, Orianne and Uhrmacher, Adelinde M. (2010) Parallel Analysis with FAMVal to Speed Up Simulation-based Model Checking. In: Fourth UKSim European Symposium on Computer Modeling and Simulation (EMS 2010), 17-19 Nov 2010, Pisa, Italy. Proceedings, published by IEEE, pp. 344-350.
Leye, Stefan and Uhrmacher, Adelinde M. (2010) A flexible and extensible architecture for experimental model validation. In: 3rd International Conference on Simulation Tools and Techniques (SIMUTOOLS 2010), 15-19 Mar 2010, Torremolinos, Malaga, Spain. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, 65:1-65:10.
Maus, Carsten and John, Mathias and Rybacki, Stefan and Uhrmacher, Adelinde M. (2010) Towards Rule-Based Multi-Level Modeling. In: 11th International Conference on Systems Biology (ICSB 2010), 10-15 Oct 2010, Edinburgh, UK. Poster.
Rybacki, Stefan and Himmelspach, Jan and Seib, Enrico and Uhrmacher, Adelinde M. (2010) Using workflows in M&S software. In: Winter Simulation Conference (WSC 2010), 05-08 Dec 2010, Baltimore, Maryland, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 535-545.
Seib, Enrico (2010) Arbeitsabläufe in der Modellierung und Simulation. Masters thesis, Institut für Informatik, Universität Rostock.
Zinn, Sabine and Gampe, Jutta and Himmelspach, Jan and Uhrmacher, Adelinde M. (2010) A DEVS model for demographic microsimulation. In: Spring Simulation Multiconference (SpringSim 2010), 11-15 Apr 2010, Orlando, Florida, USA. Proceedings, published by Society for Computer Simulation International (SCSI), San Diego, CA, USA, 146:1-146:8.
Dalle, Olivier and Ribault, Judicael and Himmelspach, Jan (2009) Design considerations for M&S software. In: Winter Simulation Conference (WSC 2009), 13-16 Dec 2009, Austin, TX, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 944-955.
Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M. (2009) Performance Issues in Evaluating Models and Designing Simulation Algorithms. In: International Workshop on High Performance Computational Systems Biology (HiBi 2009), 14-16 Oct 2010, Trento, Italy. Proceedings, published by IEEE, pp. 71-80.
Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M. (2009) An Efficient and Adaptive Mechanism for Parallel Simulation Replication. In: 23rd Workshop on Principles of Advanced and Distributed Simulation (PADS 2009), 22-25 Jun 2010, Lake Placid, New York, USA. Proceedings, published by IEEE, pp. 104-113.
Ewald, Roland and Uhrmacher, Adelinde M. and Saha, Kaustav (2009) Data mining for simulation algorithm selection. In: 2nd International Conference on Simulation Tools and Techniques for Communications, Networks and Systems (SimuTools 2009), 02-06 Mar, Rome, Italy. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, 14:1-14:10.
Henkel, Ron and Köhn, Dagmar and Peters, Andre and Maus, Carsten (2009) Similarity Measures for Computational Biological Models. In: 6th International Workshop Data Integration in the Life Sciences (DILS 2009), 20-22 Jul, Manchester, UK. Poster.
Himmelspach, Jan (2009) Toward a Collection of Principles, Techniques, and Elements of Modeling and Simulation Software. In: 2009 First International Conference on Advances in System Simulation (SIMUL 2009), September 20-25, Porto, Portugal. Proceedings,, pp. 56-61.
Himmelspach, Jan and Uhrmacher, Adelinde M. (2009) The JAMES II Framework for Modeling and Simulation. In: 2009 International Workshop on High Performance Computational Systems Biology (HiBi 2009), October 14-16, Trento, Italy. Proceedings,, pp. 101-102.
Himmelspach, Jan and Uhrmacher, Adelinde M. (2009) What contributes to the quality of simulation results? In: 2009 INFORMS Simulation Society Research Workshop, June 25-27, Coventry, U.K. Proceedings,, pp. 125-129.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim (2009) Dynamic Compartments in the Imperative π-Calculus. In: CMSB 2009: 7th International Conference on Computational Methods in Systems Biology, August 31 - September 1, Bologna, Italy. Proceedings,, pp. 235-250.
John, Mathias and Schulz, Hans-Jörg and Schumann, Heidrun and Uhrmacher, Adelinde M. and Unger, Andrea (2009) Interactive Poster: Exploring Time-Varying Hypergraphs. In: InfoVis 2009, October 11-16, Atlantic City, NJ, USA. Poster.
Köhn, Dagmar and Maus, Carsten and Henkel, Ron and Kolbe, Martin (2009) Towards Enhanced Retrieval of Biological Models through Annotation-Based Ranking. In: 6th International Workshop on Data Integration in Life Science (DILS 2009), July 20-22, Manchester, UK. Proceedings,, pp. 204-219.
Leye, Stefan and Himmelspach, Jan and Uhrmacher, Adelinde M. (2009) A Discussion on Experimental Model Validation. In: Proceedings of the UKSim'11, International Conference on Computer Modelling and Simulation, March 25-27, Cambridge, UK. Proceedings,, pp. 161-167.
Maus, Carsten and Jeschke, Matthias and Uhrmacher, Adelinde M. (2009) Spatial Multi-Level Modelling and Simulation for Systems Biology. In: CMSB 2009: 7th International Conference on Computational Methods in Systems Biology, August 31 - September 1, Bologna, Italy. Poster.
Mazemondet, Orianne and John, Mathias and Maus, Carsten and Uhrmacher, Adelinde M. and Rolfs, Arndt (2009) Integrating Diverse Reaction Types into Stochastic Models - A Signaling Pathway Case Study in the Imperative π-Calculus. In: Winter Simulation Conference, WSC 2009, December 13-16, Austin, TX, USA. Proceedings,, pp. 932-943.
Mazemondet, Orianne and John, Mathias and Maus, Carsten and Uhrmacher, Adelinde M. and Rolfs, Arndt (2009) Modeling the Cell Cycle Dependency of the Wnt/β-catenin Signaling Pathway in the Imperative π-Calculus. In: CMSB 2009: 7th International Conference on Computational Methods in Systems Biology, August 31 - September 1, Bologna, Italy. Poster.
Oertel, Yvonne (2009) ExML - ein Austauschformat für valide Experimentbeschreibungen zum Austausch zwischen verschiedenen Simulationssystemen. Diploma thesis, Institute of Computer Science, University of Rostock.
Ruddeck, Géraldine and Himmelspach, Jan and Martens, Alke (2009) Intelligent Tutoring of Modeling and Simulation Techniques. In: 2009 Winter Simulation Conference, WSC'09, December 13-16, Austin, TX, USA. Poster.
Schäfer, Andreas and John, Mathias (2009) Conceptional Modeling and Analysis of Spatio-Temporal Processes in Biomolecular Sstems. In: APCCM '09 Proceedings of the Sixth Asia-Pacific Conference on Conceptual Modeling, January 01, Wellington, New Zealand. Proceedings,, pp. 39-48.
Steiniger, Alexander (2009) Web-basiertes visuelles Monitoring von James II Simulationen. Diploma thesis, Institut für Informatik, Universität Rostock.
Uhrmacher, Adelinde M. and John, Mathias and Mazemondet, Orianne and Unger, Andrea and Rharass, Tareck and Bader, Benjamin and Rolfs, Arndt (2009) Computer Science Meets Cell Biology - GRK dIEM oSiRiS. University of Rostock.
Uhrmacher, Adelinde M. and Schulz, Hans-Jörg and Schumann, Heidrun and Schwabe, Lars and Timmermann, Dirk (2009) Regenerative systems: challenges and opportunities for modeling, simulation, and visualization. In: 4th International Conference on Performance Evaluation Methodologies and Tools, VALUETOOLS '09, Pisa, Italy, October 20-22, 2009. Proceedings,, p. 45.
Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping and Uhrmacher, Adelinde M. (2009) Experimental Analysis of Logical Process Simulation Algorithms in JAMES II. In: Winter Simulation Conference (WSC 2009), 13-16 Dec 2009, Austin, TX, USA. Proceedings, published by IEEE, Electronic ISSN: 1558-4305, pp. 1167-1179.
Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping and Uhrmacher, Adelinde M. (2009) An experimental analysis environment for logical process simulation algorithms. In: 2nd International Conference on Simulation Tools and Techniques for Communications, Networks and Systems (SimuTools 2009), 02-06 Mar, Rome, Italy. Proceedings, published by Institute for Computer Sciences, Social-Informatics and Telecommunications Engineering (ICST), Brussels, Belgium, 40:1-40:2.
Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M. (2008) An Algorithm Selection Approach for Simulation Systems. In: 22nd International Workshop on Principles of Advanced and Distributed Simulation, PADS 2008, June 3-6, Rome, Italy. Proceedings,, pp. 91-98.
Himmelspach, Jan and Ewald, Roland and Uhrmacher, Adelinde M. (2008) A flexible and scalable experimentation layer. In: Winter Simulation Conference, WSC 2008, December 7-10, Miami, Florida, USA. Proceedings,, pp. 827-835.
Jeschke, Matthias and Ewald, Roland and Park, Alfred and Fujimoto, Richard and Uhrmacher, Adelinde M. (2008) A parallel and distributed discrete event approach for spatial cell-biological simulations. SIGMETRICS Performance Evaluation Review, 35 (4), pp. 22-31.
Jeschke, Matthias and Park, Alfred and Ewald, Roland and Fujimoto, Richard and Uhrmacher, Adelinde M. (2008) Parallel and Distributed Spatial Simulation of Chemical Reactions. In: 22st International Workshop on Principles of Advanced and Distributed Simulation, PADS 2008, June 3-6, Roma, Italy. Proceedings,, pp. 51-59.
Jeschke, Matthias and Uhrmacher, Adelinde M. (2008) Multi-resolution spatial simulation for molecular crowding. In: Winter Simulation Conference, WSC 2008, December 7-10, Miami, Florida, USA. Proceedings,, pp. 1384-1392.
John, Mathias (2008) Die Modellierung von Raum und Struktur in molekularbiologischen Systemen. In: Modellierung 2008, March 12-14, Berlin, Germany. Proceedings,, pp. 221-224.
John, Mathias and Ewald, Roland and Uhrmacher, Adelinde M. (2008) A Spatial Extension to the π Calculus. Electr. Notes Theor. Comput. Sci., 194 (3), pp. 133-148.
John, Mathias and Lhoussaine, Cédric and Niehren, Joachim and Uhrmacher, Adelinde M. (2008) The Attributed Pi Calculus. In: 6th International Conference on Computational Methods in Systems Biology, CMSB 2008, October 12-15, Rostock, Germany. Proceedings,, pp. 83-102.
John, Mathias and Tominski, Christian and Schumann, Heidrun (2008) Visual and analytical extensions for the table lens. In: Conference on Visualization and Data Analysis 2008, January 28-31, San Jose, CA, USA.
Köhn, Dagmar and Heuer, Andreas and Maus, Carsten (2008) Eine Datenbanklösung für Modellwiederverwendung in der Systembiologie. In: 20. GI-Workshop Grundlagen von Datenbanken, May 13-16, Apolda, Thüringen, Germany. Proceedings,, pp. 61-65.
Leye, Stefan (2008) Grid-Inspired Simulation of Computationally Intensive Models. Diploma thesis, Institute of Computer Science, University of Rostock.
Leye, Stefan and Himmelspach, Jan and Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M. (2008) A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution. In: 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications, 2008, October 27-29, Vancouver, BC, Canada. Proceedings,, pp. 7-16.
Leye, Stefan and Uhrmacher, Adelinde M. and Priami, Corrado (2008) A Bounded-Optimistic, Parallel Beta-Binders Simulator. In: 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications, 2008, October 27-29, Vancouver, BC, Canada. Proceedings,, pp. 139-148.
Maus, Carsten and John, Mathias and Röhl, Mathias and Uhrmacher, Adelinde M. (2008) Hierarchical Modeling for Computational Biology. In: Formal Methods for Computational Systems Biology, 8th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, Advanced Lectures, June 2-7, Bertinoro, Italy. Proceedings,, pp. 81-124.
Röhl, Mathias (2008) Definition und Realisierung einer Plattform zur modellbasierten Komposition von Simulationsmodellen. PhD thesis, Institute of Computer Science, University of Rostock.
Röhl, Mathias and Uhrmacher, Adelinde M. (2008) Definition and analysis of composition structures for discrete-event models. In: Winter Simulation Conference, WSC 2008, December 7-10, Miami, Florida, USA. Proceedings,, pp. 942-950.
Schulz, Hans-Jörg and John, Mathias and Unger, Andrea and Schumann, Heidrun (2008) Interactive Poster: Table-based Visualization and Interaction for Bipartite Graphs. In: VisWeek 2008, October 19-24, Columbus, Ohio, USA. Poster.
Uhrmacher, Adelinde M. and Himmelspach, Jan and Jeschke, Matthias and John, Mathias and Leye, Stefan and Maus, Carsten and Röhl, Mathias and Ewald, Roland (2008) One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II. In: 1st International Workshop Formal Methods in Systems Biology, FMSB 2008, June 4-5, Cambridge, UK. Proceedings,, pp. 123-138.
Uhrmacher, Adelinde M. and Rolfs, Arndt and Frahm, Jana (2007) DFG Research Training Group 1387/1: dIEM oSiRiS - Integrative Development of Modelling and Simulation Methods for Regenerative Systems (DFG Graduiertenkolleg 1387/1: dIEM oSiRiS - Die integrative Entwicklung von Modellierungs- und Simulationsmethoden für regenerative Systeme). DE GRUYTER Oldenbourg.
Uhrmacher, Adelinde M. and Himmelspach, Jan and Röhl, Mathias and Ewald, Roland (2006) Introducing variable ports and multi-couplings for cell biological modeling in DEVS. In: Winter Simulation Conference, WSC 2006, December 3-6, Monterey, California, USA. Proceedings,, pp. 832-840.
