2023

• Ruscheinski, Andreas, Anna Lena Reimler, Roland Ewald and Adelinde M. Uhrmacher:
  Towards Analyzing the Reclassification Dynamics of ClinVar Variants.
  bioRxiv preprint
  [pdf] [view online] [abstract] [bibtex]
  ×
  

  Towards Analyzing the Reclassification Dynamics of ClinVar Variants

                                      
    @misc{Ruscheinski2023,
      title = {Towards {Analyzing} the {Reclassification} {Dynamics} of {ClinVar} {Variants}},
      copyright = {© 2023, Posted by Cold Spring Harbor Laboratory. This pre-print is available under a Creative Commons License (Attribution-NonCommercial-NoDerivs 4.0 International), CC BY-NC-ND 4.0, as described at http://creativecommons.org/licenses/by-nc-nd/4.0/},
      url = {https://www.biorxiv.org/content/10.1101/2023.01.24.525342v2},
      doi = {10.1101/2023.01.24.525342},
      abstract = {ClinVar aggregates information about genetic variants and their relation to human diseases and forms a valuable resource for clinical diagnostics. The assessment of variants, e.g., as being benign or pathogenetic, changes over time. We collected variant classification histories of ClinVar releases and used those to derive discrete-time Markov chains to investigate the reclassification dynamics of variants in ClinVar in terms of transition probabilities between ClinVar releases and reclassifications.},
      language = {en},
      urldate = {2023-02-19},
      publisher = {bioRxiv},
      author = {Ruscheinski, Andreas and Reimler, Anna Lena and Ewald, Roland and Uhrmacher, Adelinde M.},
      month = jan,
      year = {2023},
      note = {Pages: 2023.01.24.525342
  Section: New Results},
      file = {Full Text PDF:/home/roland/Zotero/storage/GCY8V8Y7/Ruscheinski et al. - 2023 - Towards Analyzing the Reclassification Dynamics of.pdf:application/pdf},
  }
  

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  Towards Analyzing the Reclassification Dynamics of ClinVar Variants

  ClinVar aggregates information about genetic variants and their relation to human diseases and forms a valuable resource for clinical diagnostics. The assessment of variants, e.g., as being benign or pathogenetic, changes over time. We collected variant classification histories of ClinVar releases and used those to derive discrete-time Markov chains to investigate the reclassification dynamics of variants in ClinVar in terms of transition probabilities between ClinVar releases and reclassifications.

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2022

• Hallermayr, Ariane, Teresa M. Neuhann, Verena Steinke-Lange, Florentine Scharf, Andreas Laner, Roland Ewald, Ben Liesfeld, Elke Holinski-Feder and Julia M. A. Pickl:
  Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants.
  Frontiers in Oncology Volume 12
  [pdf] [view online] [abstract] [bibtex]
  ×
  

  Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants

                                      
    @ARTICLE{Hallermayr2022,
      title = {Highly sensitive liquid biopsy {Duplex} sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants},
      volume = {12},
      issn = {2234-943X},
      url = {https://www.frontiersin.org/articles/10.3389/fonc.2022.1014592},
      abstract = {BackgroundLiquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients.MethodsWe developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established.ResultsWe investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100\% sensitivity and 92.3\% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7\% sensitivity and 100\% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5\% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25\% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5\% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches.ConclusionOur flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases.},
      urldate = {2023-02-19},
      journal = {Frontiers in Oncology},
      author = {Hallermayr, Ariane and Neuhann, Teresa M. and Steinke-Lange, Verena and Scharf, Florentine and Laner, Andreas and Ewald, Roland and Liesfeld, Ben and Holinski-Feder, Elke and Pickl, Julia M. A.},
      year = {2022},
      file = {Full Text PDF:/home/roland/Zotero/storage/4C7YTN9L/Hallermayr et al. - 2022 - Highly sensitive liquid biopsy Duplex sequencing c.pdf:application/pdf},
  }
  

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  ×
  

  Highly sensitive liquid biopsy Duplex sequencing complements tissue biopsy to enhance detection of clinically relevant genetic variants

  Background: Liquid biopsy (LB) is a promising complement to tissue biopsy for detection of clinically relevant genetic variants in cancer and mosaic diseases. A combined workflow to enable parallel tissue and LB analysis is required to maximize diagnostic yield for patients.
  Methods: We developed and validated a cost-efficient combined next-generation sequencing (NGS) workflow for both tissue and LB samples, and applied Duplex sequencing technology for highly accurate detection of low frequency variants in plasma. Clinically relevant cutoffs for variant reporting and quantification were established.
  Results: We investigated assay performance characteristics for very low amounts of clinically relevant variants. In plasma, the assay achieved 100% sensitivity and 92.3% positive predictive value (PPV) for single nucleotide variants (SNVs) and 91.7% sensitivity and 100% PPV for insertions and deletions (InDel) in clinically relevant hotspots with 0.5-5% variant allele frequencies (VAFs). We further established a cutoff for reporting variants (i.e. Limit of Blank, LOB) at 0.25% VAF and a cutoff for quantification (i.e. Limit of Quantification, LOQ) at 5% VAF in plasma for accurate clinical interpretation of analysis results. With our LB approach, we were able to identify the molecular cause of a clinically confirmed asymmetric overgrowth syndrome in a 10-year old child that would have remained undetected with tissue analysis as well as other molecular diagnostic approaches. Conclusions
  Our flexible and cost-efficient workflow allows analysis of both tissue and LB samples and provides clinically relevant cutoffs for variant reporting and precise quantification. Complementing tissue analysis by LB is likely to increase diagnostic yield for patients with molecular diseases.

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2021

• Ruscheinski, Andreas, Anna Lena Reimler, Roland Ewald, and Adelinde M. Uhrmacher:
  VPMBench: A Test Bench for Variant Prioritization Methods.
  BMC Bioinformatics 22, no. 1 (543)
  [pdf] [view online] [abstract] [bibtex]
  ×
  

  VPMBench: A Test Bench for Variant Prioritization Methods

                                      
    @ARTICLE{Ruscheinski2021,
    author = {Ruscheinski, Andreas and Reimler, Anna Lena and Ewald, Roland and Uhrmacher, Adelinde M.},
    title = {VPMBench: A Test Bench for Variant Prioritization Methods.},
    journal = {BMC Bioinformatics},
    year = {2021},
    month = {nov}
    issue = {1},
    volume = {22},
    pages= {. “”  22, no. 1 (November 8, 2021): 543. https://doi.org/10.1186/s12859-021-04458-0.},
    abstract = {Background: Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort.
    Results: The open-source test bench “VPMBench” automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization.
    Conclusions: VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.},
    publisher = {BioMed Central},
    preprint = {docs/2021_Ewald_AIPlanning.pdf},
    doi = {https://doi.org/10.1186/s12859-021-04458-0},
    }
  

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  ×
  

  VPMBench: A Test Bench for Variant Prioritization Methods

  Background
  Clinical diagnostics of whole-exome and whole-genome sequencing data requires geneticists to consider thousands of genetic variants for each patient. Various variant prioritization methods have been developed over the last years to aid clinicians in identifying variants that are likely disease-causing. Each time a new method is developed, its effectiveness must be evaluated and compared to other approaches based on the most recently available evaluation data. Doing so in an unbiased, systematic, and replicable manner requires significant effort.
  Results
  The open-source test bench “VPMBench” automates the evaluation of variant prioritization methods. VPMBench introduces a standardized interface for prioritization methods and provides a plugin system that makes it easy to evaluate new methods. It supports different input data formats and custom output data preparation. VPMBench exploits declaratively specified information about the methods, e.g., the variants supported by the methods. Plugins may also be provided in a technology-agnostic manner via containerization.
  Conclusions
  VPMBench significantly simplifies the evaluation of both custom and published variant prioritization methods. As we expect variant prioritization methods to become ever more critical with the advent of whole-genome sequencing in clinical diagnostics, such tool support is crucial to facilitate methodological research.

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2019

• Büttner, Benjamin et al.:
  Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders.
  bioarxiv.org Preprint
  [view online] [abstract] [bibtex]
  ×
  

  Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders

                                      
  @article{Buettner2019,
  author = {B{\"u}ttner, Benjamin and Martin, Sonja and Finck, Anja and Arelin, Maria and Baade-B{\"u}ttner, Carolin and Bartolomaeus, Tobias and Bauer, Peter and Bertsche, Astrid and Bernhard, Matthias K. and Biskup, Saskia and Donato, Nataliya Di and Elgizouli, Magdeldin and Ewald, Roland and Heine, Constanze and Hellenbroich, Yorck and Hentschel, Julia and Hoffjan, Sabine and Horn, Susanne and Hornemann, Frauke and Huhle, Dagmar and Kamphausen, Susanne B. and Kiess, Wieland and Krey, Ilona and Kuechler, Alma and Liesfeld, Ben and Merkenschlager, Andreas and Mitter, Diana and Muschke, Petra and Pf{\"a}ffle, Roland and Polster, Tilman and Schanze, Ina and Schlump, Jan-Ulrich and Syrbe, Steffen and Wieczorek, Dagmar and Zenker, Martin and Lemke, Johannes R. and Duc, Diana Le and Platzer, Konrad and Jamra, Rami Abou},
      title = {Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders},
      year = {2019},
      doi = {10.1101/588517},
      publisher = {Cold Spring Harbor Laboratory},
      URL = {https://www.biorxiv.org/content/early/2019/03/26/588517},
      eprint = {https://www.biorxiv.org/content/early/2019/03/26/588517.full.pdf},
      journal = {bioRxiv}
  }
  

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  ×
  

  Scientific evaluation of negative exome sequencing followed by systematic scoring of candidate genes to decipher the genetics of neurodevelopmental disorders

  Background
  Deciphering the monogenetic causes of neurodevelopmental disorders (NDD) is an important milestone to offer personalized care. But the plausibility of reported candidate genes in exome studies often remains unclear, which slows down progress in the field.
  Methods
  We performed exome sequencing (ES) in 198 cases of NDD. Cases that remained unresolved (n=135) were re-investigated in a research setting. We established a candidate scoring system (CaSc) based on 12 different parameters reflecting variant and gene attributes as well as current literature to rank and prioritize candidate genes.
  Results
  In this cohort, we identified 158 candidate variants in 148 genes with CaSc ranging from 2 to 11.7. Only considering the top 15% of candidates, 14 genes were already published or funneled into promising validation studies.
  Conclusions
  We promote that in an approach of case by case re-evaluation of primarily negative ES, systematic and standardized scoring of candidate genes can and should be applied. This simple framework enables better comparison, prioritization, and communication of candidate genes within the scientific community. This would represent an enormous benefit if applied to the tens of thousands of negative ES performed in routine diagnostics worldwide and speed up deciphering the monogenetic causes of NDD.

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2015

• Haack, Fiete and Lemcke, Heiko and Ewald, Roland and Rharass, Tareck and Uhrmacher, Adelinde M :
  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)
  [view online] [abstract] [bibtex]
  ×
  

  Spatio-temporal model of endogenous ROS and raft-dependent Wnt/beta-catenin signaling driving cell fate commitment in human neural progenitor cells

                                      
  @article{Haack2015,
  author = {Haack, Fiete and Lemcke, Heiko and Ewald, Roland and Rharass, Tareck and Uhrmacher, Adelinde M}, 
  year = {2015}, 
  title = {Spatio-temporal model of endogenous ROS and raft-dependent Wnt/beta-catenin signaling driving cell fate commitment in human neural progenitor cells}, 
  pages = {e1004106}
  doi = {http://dx.doi.org/10.1371/journal.pcbi.1004106}, 
  journal = {PLOS Computational Biology}, 
  volume = {11}, 
  number = {3}, 
  }
  

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  ×
  

  Spatio-temporal model of endogenous ROS and raft-dependent Wnt/beta-catenin signaling driving cell fate commitment in human neural progenitor cells

  Canonical WNT/beta-catenin signaling is a central pathway in embryonic development, but it is also connected to a number of cancers and developmental disorders. Here we apply a combined in-vitro and in-silico approach to investigate the spatio-temporal regulation of WNT/beta-catenin signaling during the early neural differentiation process of human neural progenitors cells (hNPCs), which form a new prospect for replacement therapies in the context of neurodegenerative diseases. Experimental measurements indicate a second signal mechanism, in addition to canonical WNT signaling, being involved in the regulation of nuclear beta-catenin levels during the cell fate commitment phase of neural differentiation. We find that the biphasic activation of beta-catenin signaling observed experimentally can only be explained through a model that combines Reactive Oxygen Species (ROS) and raft dependent WNT/beta-catenin signaling. Accordingly after initiation of differentiation endogenous ROS activates DVL in a redox-dependent manner leading to a transient activation of down-stream beta-catenin signaling, followed by continuous auto/paracrine WNT signaling, which crucially depends on lipid rafts. Our simulation studies further illustrate the elaborate spatio-temporal regulation of DVL, which, depending on its concentration and localization, may either act as direct inducer of the transient ROS/beta-catenin signal or as amplifier during continuous auto-/parcrine WNT/beta-catenin signaling. In addition we provide the first stochastic computational model of WNT/beta-catenin signaling that combines membrane-related and intracellular processes, including lipid rafts/receptor dynamics as well as WNT- and ROS-dependent beta-catenin activation. The model's predictive ability is demonstrated under a wide range of varying conditions for in-vitro and in-silico reference data sets. Our in-silico approach is realized in a multi-level rule-based language, that facilitates the extension and modification of the model. Thus, our results provide both new insights and means to further our understanding of canonical WNT/beta-catenin signaling and the role of ROS as intracellular signaling mediator.

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• Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M :
  Automatic Runtime Adaptation for Component-Based Simulation Algorithms.
  ACM Transactions on Modeling and Computer Simulation 26 (1)
  [view online] [abstract] [bibtex]
  ×
  

  Automatic Runtime Adaptation for Component-Based Simulation Algorithms

                                      
  @article{Helms2015,
  author = {Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M}, 
  year = {2015}, 
  title = {Automatic Runtime Adaptation for Component-Based Simulation Algorithms}, 
  pages = {1-24}, 
  publisher = {ACM}, 
  journal = {ACM Transactions on Modeling and Computer Simulation}, 
  volume = {26}, 
  number = {1}, 
  doi = {http://dx.doi.org/10.1145/2821509}, }
  

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  ×
  

  Automatic Runtime Adaptation for Component-Based Simulation Algorithms

  The state and structure of a model may vary during a simulation and, thus, also its computational demands. Adapting simulation algorithms to these demands at runtime can therefore improve their performance. While this is a general and cross-cutting concern, only few simulation systems offer reusable support for this kind of runtime adaptation. We present a flexible and generic mechanism for the runtime adaptation of component-based simulation algorithms.Itencapsulates simulation algorithms applicable to agiven problem and employs reinforcement learning to explore the algorithms' performance during a simulation run. We evaluate our approach on a modeling formalism from computational biology and on a benchmark model defined in PDEVS, thereby investigating a broad range of options for improving its learning capabilities.

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2014

• Barros, Fernando and Perumalla, Kalyan and Ewald, Roland (eds.) :
  Proceedings of the 7th International ICST Conference on Simulation Tools and Techniques.
  ICST Proceedings
  [view online] [bibtex]
  ×
  

  Proceedings of the 7th International ICST Conference on Simulation Tools and Techniques

                                      
  @proceedings{Barros2014,
  author = {Barros, Fernando and Perumalla, Kalyan and Ewald, Roland (eds.)}, 
  year = {2014}, 
  title = {Proceedings of the 7th International ICST Conference on Simulation
  Tools and Techniques}, 
  booktitle = {ICST}, 
  publisher = {ICST}, 
  editor = {Barros, Fernando and Perumalla, Kalyan and Ewald, Roland}, 
  note = {Proceedings}, 
  }
  

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  Proceedings of the 7th International ICST Conference on Simulation Tools and Techniques

  Close
• Ewald, Roland :
  Using AI Planning to Automate the Performance Analysis of Simulators.
  Proceedings of the 7th International ICST Conference on Simulation Tools and Techniques (SIMUTools)
  [preprint] [talk slides] [abstract] [bibtex]
  ×
  

  Using AI Planning to Automate the Performance Analysis of Simulators

                                      
  @inproceedings{Ewald2014a,
  author = {Ewald, Roland}, 
  year = {2014}, 
  title = {Using AI Planning to Automate the Performance Analysis of Simulators}, 
  booktitle = {Proceedings of the 7th International ICST Conference on Simulation
  Tools and Techniques (SIMUTools)}, 
  publisher = {ICST}, 
  }
  

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  ×
  

  Using AI Planning to Automate the Performance Analysis of Simulators

  Analyzing simulation algorithm performance is cumbersome: execute some runs, observe a performance metric, and analyze the results. Often, the results motivate follow-up experiments, which in turn may lead to additional experiments, and so on. This time-consuming and error-prone process can be automated with planning approaches from artificial intelligence, making simulator performance analysis more convenient and rigorous. This paper introduces ALeSiA, a prototypical system for automatic simulator performance analysis. It is independent of any specific simulation system and realizes a hypothesis-driven approach to evaluate performance.

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• Ewald, Roland and Uhrmacher, Adelinde M. :
  SESSL: A Domain-Specific Language for Simulation Experiments.
  ACM Transactions on Modeling and Computer Simulation 24 (2)
  [preprint] [view online] [abstract] [bibtex]
  ×
  

  SESSL: A Domain-Specific Language for Simulation Experiments

                                      
  @article{Ewald2014,
  author = {Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2014}, 
  title = {SESSL: A Domain-Specific Language for Simulation Experiments}, 
  journal = {ACM Transactions on Modeling and Computer Simulation}, 
  volume = {24}, 
  number = {2}, 
  doi = {http://dx.doi.org/10.1145/2567895}, }
  

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  ×
  

  SESSL: A Domain-Specific Language for Simulation Experiments

  This paper introduces SESSL (Simulation Experiment Specification via a Scala Layer), an embedded domain-specific language for simulation experiments. It serves as an additional software layer between users and simulation systems and is implemented in Scala. SESSL supports multiple simulation systems and offers various features, e.g., for experiment design, performance analysis, result reporting, and simulation-based optimization. It supports 'cutting-edge' experiments by allowing to add custom code, enables a reuse of functionality across simulation systems, and improves the reproducibility of simulation experiments.

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• Leye, Stefan and Ewald, Roland and Uhrmacher, Adelinde M. :
  Composing Problem Solvers for Simulation Experimentation: A Case Study on Steady State Estimation.
  PLoS ONE 9 (4), e91948
  [view online] [abstract] [bibtex]
  ×
  

  Composing Problem Solvers for Simulation Experimentation: A Case Study on Steady State Estimation

                                      
  @article{Leye2014,
  author = {Leye, Stefan and Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2014}, 
  title = {Composing Problem Solvers for Simulation Experimentation: A Case
  Study on Steady State Estimation}, 
  journal = {PLoS ONE}, 
  volume = {9 (4), e91948}, 
  }
  

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  ×
  

  Composing Problem Solvers for Simulation Experimentation: A Case Study on Steady State Estimation

  Simulation experiments involve various sub-tasks, e.g., parameter optimization, simulation execution, or output data analysis. Many algorithms can be applied to such tasks, but their performance depends on the given problem. Steady-state estimation in systems biology is a typical example for this: several estimators have been proposed, each with its own (dis-)advantages. Experimenters, therefore, must choose from the available options, even though they may not be aware of the consequences. To support those users, we propose a general scheme to aggregate such algorithms to so-called synthetic problem solvers, which exploit algorithm differences to improve overall performance. Our approach subsumes various aggregation mechanisms, supports automatic configuration from training data (\eg via ensemble learning or portfolio selection), and extends the plug-in system of the open source modeling and simulation framework James II. We show the benefits of our approach by applying it to steady-state estimation for cell-biological models.

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• Peng, Danhua and Ewald, Roland and Uhrmacher, Adelinde M. :
  Towards Semantic Model Composition via Experiments.
  Proceedings of the 2014 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS)
  [preprint] [view online] [abstract] [bibtex]
  ×
  

  Towards Semantic Model Composition via Experiments

                                      
  @inproceedings{Peng2014,
  author = {Peng, Danhua and Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2014}, 
  title = {Towards Semantic Model Composition via Experiments}, 
  booktitle = {Proceedings of the 2014 ACM SIGSIM Conference on Principles of Advanced
  Discrete Simulation (PADS)}, 
  }
  

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  ×
  

  Towards Semantic Model Composition via Experiments

  Unambiguous experiment descriptions are increasingly required for model publication, as they contain information important for reproducing simulation results. In the context of model composition, this information can be used to generate experiments for the composed model. If the original experiment descriptions specify which model property they refer to, we can then execute the generated experiments and assess the validity of the composed model by evaluating their results. Thereby, we move the attention to describing properties of a model's behavior and the conditions under which these hold, i.e., its semantics. We illuminate the potential of this concept by considering the composition of Lotka-Volterra models. In a first prototype realized for JAMES II, we use ML-Rules to describe and execute the Lotka-Volterra models and SESSL for specifying the original experiments. Model properties are described in continuous stochastic logic, and we use statistical model checking for their evaluation. Based on this, experiments to check whether these properties hold for the composed model are automatically generated and executed.

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2013

• Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M :
  A Generic Adaptive Simulation Algorithm for Component-based Simulation Systems.
  Proceedings of the 2013 ACM SIGSIM Conference on Principles of Advanced Discrete Simulation (PADS)
  [view online] [abstract] [bibtex]
  ×
  

  A Generic Adaptive Simulation Algorithm for Component-based Simulation Systems

                                      
  @inproceedings{Helms2013,
  author = {Helms, Tobias and Ewald, Roland and Rybacki, Stefan and Uhrmacher, Adelinde M}, 
  year = {2013}, 
  title = {A Generic Adaptive Simulation Algorithm for Component-based Simulation
  Systems}, 
  booktitle = {Proceedings of the 2013 ACM SIGSIM Conference on Principles of Advanced
  Discrete Simulation (PADS)}, 
  pages = {11-22}, 
  publisher = {ACM}, 
  doi = {http://dx.doi.org/10.1145/2486092.2486095}, }
  

  Close
  ×
  

  A Generic Adaptive Simulation Algorithm for Component-based Simulation Systems

  The state of a model may strongly vary during simulation, and with it also the simulation's computational demands. Adapting the simulation algorithm to these demands at runtime can therefore improve the overall performance. Although this is a general and cross-cutting concern, only few simulation systems offer re-usable support for this kind of runtime adaptation. We present a flexible and generic mechanism for the runtime adaptation of component-based simulation algorithms. It encapsulates simulation algorithms applicable to a given problem and employs reinforcement learning to explore the algorithms' suitability during a simulation run. We evaluate the approach by executing models from two modeling formalisms used in computational biology.

  Close
• Nähring, Sebastian and Maus, Carsten and Ewald, Roland and Uhrmacher, Adelinde M :
  From Standardized Modeling Formats to Modeling Languages and back --- an Exploration based on SBML and ML-Rules.
  Proceedings of the 2013 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  From Standardized Modeling Formats to Modeling Languages and back --- an Exploration based on SBML and ML-Rules

                                      
  @inproceedings{Naehring2013,
  author = {Nähring, Sebastian and Maus, Carsten and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2013}, 
  title = {From Standardized Modeling Formats to Modeling Languages and back
  --- an Exploration based on SBML and ML-Rules}, 
  booktitle = {Proceedings of the 2013 Winter Simulation Conference}, 
  }
  

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  ×
  

  From Standardized Modeling Formats to Modeling Languages and back --- an Exploration based on SBML and ML-Rules

  Standardized model exchange formats give practitioners the freedom to choose the most suitable tool and facilitate both cross-validation and reproduction of simulation results. On the other hand, standardization necessarily implies a compromise between the capabilities of individual modeling languages and a common ground of concepts and underlying assumptions of the given application domain. This compromise often leads to a mismatch of expressiveness between modeling language and exchange format, which should be resolved automatically, e.g., by offering a transformation. We explore the challenges of such an approach for the Systems Biology Markup Language (SBML), a well-established model format in systems biology, and ML-Rules, a rule-based modeling language for describing cell biological systems at multiple interrelated levels. Our transformation approach can be extended both in terms of the heuristics it employs and in terms of the modeling formalisms it supports.

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• Schützel, Johannes and Ewald, Roland and Uhrmacher, Adelinde M :
  A General Foundation for Formalism-Specific Instrumentation Languages.
  Proceedings of the 2013 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  A General Foundation for Formalism-Specific Instrumentation Languages

                                      
  @misc{Schuetzel2013,
  author = {Schützel, Johannes and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2013}, 
  title = {A General Foundation for Formalism-Specific Instrumentation Languages}, 
  booktitle = {Proceedings of the 2013 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

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  ×
  

  A General Foundation for Formalism-Specific Instrumentation Languages

  Experimenters need to configure the data collection performed during a simulation run, as this avoids overly large output data sets and the overhead of collecting them. Instrumentation languages address this problem by allowing experimenters to specify the data of interest. Such languages typically focus on a specific modeling formalism. While this allows for a more expressive syntax, it also prohibits their application to other formalisms. To resolve this trade-off, we propose a formalism-independent model of the instrumentation semantics and use it as a basis for developing embedded domain-specific languages (DSLs). Our instrumentation DSLs share common code, allow to add formalism-specific syntax, and are easy to extend.

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• Wienß, Jonathan and Stein, Michael and Ewald, Roland :
  Evaluating Simulation Software Components with Player Rating Systems.
  Proceedings of the 6th International ICST Conference on Simulation Tools and Techniques (SIMUTools)
  [view online] [abstract] [bibtex]
  ×
  

  Evaluating Simulation Software Components with Player Rating Systems

                                      
  @inproceedings{Wienss2013,
  author = {Wienß, Jonathan and Stein, Michael and Ewald, Roland}, 
  year = {2013}, 
  title = {Evaluating Simulation Software Components with Player Rating Systems}, 
  booktitle = {Proceedings of the 6th International ICST Conference on Simulation
  Tools and Techniques (SIMUTools)}, 
  }
  

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  ×
  

  Evaluating Simulation Software Components with Player Rating Systems

  In component-based simulation systems, simulation runs are usually executed by combinations of distinct components, each solving a particular sub-task. If multiple components are available for a given sub-task (e.g., different event queue implementations), a simulation system may rely on an automatic selection mechanism, on a user decision, or --- if neither is available --- on a predefined default component. However, deciding upon a default component for each kind of sub-task is difficult: such a component should work well across various application domains and various combinations with other components. Furthermore, the performance of individual components cannot be evaluated easily, since performance is typically measured for component combinations as a whole (e.g., the execution time of a simulation run). Finally, the selection of default components should be dynamic, as new and potentially superior components may be deployed to the system over time. We illustrate how player rating systems for team-based games can solve the above problems and evaluate our approach with an implementation of the TrueSkill(tm) rating system (Herbrich et al, 2007), applied in the context of the open-source modeling and simulation framework JAMES II. We also show how such systems can be used to steer performance analysis experiments for component ranking. Paper and talk slides are available online.

  Close

2012

• Bohk, Christina and Ewald, Roland and Rau, Roland :
  Towards a Generalized Subpopulation Support for Stochastic Population Projections.
  Proceedings of the 2012 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  Towards a Generalized Subpopulation Support for Stochastic Population Projections

                                      
  @misc{Bohk2012,
  author = {Bohk, Christina and Ewald, Roland and Rau, Roland}, 
  year = {2012}, 
  title = {Towards a Generalized Subpopulation Support for Stochastic Population
  Projections}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  Towards a Generalized Subpopulation Support for Stochastic Population Projections

  Demographic heterogeneity, i.e. differing mortality and fertility among subpopulations, is an important issue in stochastic demographic forecasting. Common approaches typically use the variables age and sex to construct subpopulations, but this might be insufficient and induce projection error. Many studies show significant differences in mortality and fertility among people with and without migration background, but also among people with different level of education or country of origin. So far, our model projects the autochthonous population, immigrants, emigrants, and their descendant generations with separate mortality and fertility. Hence, the subpopulations are build with the variables age, sex, and migration status. In this paper, we extend the model so that a forecaster can project an unlimited number of subpopulations. Next to age, sex, and migration background, a forecaster can use other characteristics like reason of migration or employment to construct subpopulations, and thus to increase projection accuracy.

  Close
• Engelke, Robert and Ewald, Roland :
  Configuring Simulation Algorithms with ParamILS.
  Proceedings of the 2012 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  Configuring Simulation Algorithms with ParamILS

                                      
  @misc{Engelke2012,
  author = {Engelke, Robert and Ewald, Roland}, 
  year = {2012}, 
  title = {Configuring Simulation Algorithms with ParamILS}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  Configuring Simulation Algorithms with ParamILS

  Simulation algorithms often expose various numerical parameters, e.g., to control the size of auxiliary data structures or to configure certain heuristics. While this allows to fine-tune a simulator to a given model, it also makes simulator configuration more complex. For example, determining suitable default parameters from a multi-dimensional parameter space is challenging, as these parameters shall work well on a broad range of models. Instead of manually selecting parameter values, the configuration space of a simulation algorithm can also be searched automatically. We investigate how well ParamILS (Hutter et al. 2009), an iterated local search algorithm for algorithm configuration, can be applied to simulation algorithms, and discuss its implementation in context of the open-source modeling and simulation framework JAMES II.

  Close
• Ewald, Roland and Uhrmacher, Adelinde M. :
  Setting up Simulation Experiments with SESSL.
  Proceedings of the 2012 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  Setting up Simulation Experiments with SESSL

                                      
  @misc{Ewald2012,
  author = {Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2012}, 
  title = {Setting up Simulation Experiments with SESSL}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  pages = {379:1--379:2}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  Setting up Simulation Experiments with SESSL

  Setting up simulation experiments is hard, even more so as simulation systems usually offer only custom interfaces for this task (e.g., a graphical user interface or a programming interface). This steepens the learning curve for experimenters, who have to get accustomed with the idiosyncrasy of each simulation system they want to experiment with. It also makes cross-validation experiments between simulation systems cumbersome, since the same experiment needs to be set up for each system from scratch. In the following, we give a brief overview of SESSL, a domain-specific language for simulation experiments. SESSL addresses these issues by providing a common interface to set up simulation experiments in a more declarative manner, i.e., specifying what to do, not how to do it. Therefore, SESSL can also be used for documenting and reproducing simulation experiments.

  Close
• Helms, Tobias and Rybacki, Stefan and Ewald, Roland and Uhrmacher, Adelinde M :
  An Adaptive Simulator for ML-Rules.
  Proceedings of the 2012 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  An Adaptive Simulator for ML-Rules

                                      
  @misc{Helms2012,
  author = {Helms, Tobias and Rybacki, Stefan and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2012}, 
  title = {An Adaptive Simulator for ML-Rules}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  An Adaptive Simulator for ML-Rules

  Even the most carefully configured simulation algorithm may perform badly unless its configuration is adapted to the dynamics of the model. To overcome this problem, we apply methods from reinforcement learning to continuously re-configure an ML-Rules simulator at runtime. ML-Rules is a rule-based modeling language primarily targeted at multi-level microbiological systems. Our results show that, for models with sufficiently diverse dynamics, an adaptation of the simulator configuration may even outperform the best-performing non-adaptive configuration (which is typically unknown anyhow).

  Close
• Luboschik, Martin and Rybacki, Stefan and Ewald, Roland and Schwarze, Benjamin and Schumann, Heidrun and Uhrmacher, Adelinde M. :
  Interactive Visual Exploration of Simulator Accuracy: A Case Study for Stochastic Simulation Algorithms.
  Proceedings of the 2012 Winter Simulation Conference Invited Paper
  [view online] [abstract] [bibtex]
  ×
  

  Interactive Visual Exploration of Simulator Accuracy: A Case Study for Stochastic Simulation Algorithms

                                      
  @inproceedings{Luboschik2012,
  author = {Luboschik, Martin and Rybacki, Stefan and Ewald, Roland and Schwarze, Benjamin and Schumann, Heidrun and Uhrmacher, Adelinde M.}, 
  year = {2012}, 
  title = {Interactive Visual Exploration of Simulator Accuracy: A Case Study
  for Stochastic Simulation Algorithms}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  note = {Invited Paper}, 
  }
  

  Close
  ×
  

  Interactive Visual Exploration of Simulator Accuracy: A Case Study for Stochastic Simulation Algorithms

  Visual Analytics offers various interesting methods to explore high dimensional data interactively. In this paper we investigate how it can be applied to support experimenters and developers of simulation software conducting simulation studies. In particular the usage and development of approximate simulation algorithms poses several practical problems, e.g., estimating the impact of algorithm parameters on accuracy or detecting faulty implementations. To address some of those problems, we present an approach that allows to relate configurations and accuracy visually and exploratory. The approach is evaluated by a brief case study, focusing on the accuracy of Stochastic Simulation Algorithms.

  Close
• Nähring, Sebastian and Maus, Carsten and Ewald, Roland and Uhrmacher, Adelinde M :
  Automated Transformation Between Modeling Languages with Different Expressiveness: Challenges and Results From a Use Case with SBML and ML-Rules.
  Proceedings of the 2012 Winter Simulation Conference Poster
  [view full abstract online] [abstract] [bibtex]
  ×
  

  Automated Transformation Between Modeling Languages with Different Expressiveness: Challenges and Results From a Use Case with SBML and ML-Rules

                                      
  @misc{Naehring2012,
  author = {Nähring, Sebastian and Maus, Carsten and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2012}, 
  title = {Automated Transformation Between Modeling Languages with Different
  Expressiveness: Challenges and Results From a Use Case with SBML
  and ML-Rules}, 
  booktitle = {Proceedings of the 2012 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  Automated Transformation Between Modeling Languages with Different Expressiveness: Challenges and Results From a Use Case with SBML and ML-Rules

  Automated transformation between modeling languages is often useful, e.g., to make tools (like simulators) based on one language applicable to models defined in other languages. However, several problems arise when the expressive powers of the modeling languages differ. We consider the automated transformation between models specified in the systems biology markup language (SBML) and ML-Rules, a rule-based multilevel modeling language. While both languages allow for modeling aspects that cannot be expressed in its counterpart and thus prevent a complete and fully automated transformation, it is still possible to transform many useful classes of models. Even more models can be transformed by relying on certain heuristics or user input.

  Close

2011

• Ewald, Roland :
  Automatic Algorithm Selection for Complex Simulation Problems.
  University of Rostock, published by Vieweg + Teubner PhD Thesis
  [preprint] [view online] [abstract] [bibtex]
  ×
  

  Automatic Algorithm Selection for Complex Simulation Problems

                                      
  @phdthesis{Ewald2010Dis,
  author = {Ewald, Roland}, 
  year = {2011}, 
  title = {Automatic Algorithm Selection for Complex Simulation Problems}, 
  booktitle = {University of Rostock, published by Vieweg + Teubner}, 
  note = {PhD Thesis}, 
  }
  

  Close
  ×
  

  Automatic Algorithm Selection for Complex Simulation Problems

  To select the most suitable simulation algorithm for a given task is often difficult. This is due to intricate interactions between model features, implementation details, and runtime environment, which may strongly affect the overall performance. An automated selection of simulation algorithms supports users in setting up simulation experiments, without demanding expert knowledge on simulation. The first part of the thesis surveys existing approaches to solve the algorithm selection problem and discusses techniques to analyze simulation algorithm performance. A unified categorization of existing algorithm selection techniques is worked out, as these stem from various research domains (e.g., finance, artificial intelligence). The second part introduces a software framework for automatic simulation algorithm selection and describes its constituents, as well as their integration into the modeling and simulation framework JAMES II. The implemented selection mechanisms are able to cope with three situations: a) no prior knowledge is available, b) the impact of problem features on performance is unknown, and c) a relationship between problem features and algorithm performance can be established empirically. An experimental evaluation of the developed methods concludes the thesis. It is shown that an automated algorithm selection may significantly increase the overall performance of a simulation system. Some of the presented mechanisms also support the research on simulation methods, as they facilitate their development and evaluation.

  Close
• Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M :
  Exploring the Performance of Spatial Stochastic Simulation Algorithms.
  Journal of Computational Physics 230 (7)
  [preprint] [view online] [abstract] [bibtex]
  ×
  

  Exploring the Performance of Spatial Stochastic Simulation Algorithms

                                      
  @article{Jeschke2011,
  author = {Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2011}, 
  title = {Exploring the Performance of Spatial Stochastic Simulation Algorithms}, 
  pages = {2562-2574}, 
  journal = {Journal of Computational Physics}, 
  volume = {230}, 
  number = {7}, 
  }
  

  Close
  ×
  

  Exploring the Performance of Spatial Stochastic Simulation Algorithms

  Since the publication of Gillespie's direct method, diverse methods have been developed to improve the performance of stochastic simulation methods and to enter the spatial realm. In this paper we discuss a spatial tau-leaping variant (Stau) that extends the basic leap method. Stau takes reaction and both outgoing and incoming diffusion events into account when calculating a leap candidate. A performance analysis shall reveal details on the achieved success in balancing speed and accuracy in comparison to other methods. However, performance analysis of spatial stochastic algorithms requires significant effort --- it is crucial to choose suitable (benchmark) models and to carefully define model and simulation setups that take problem and simulation design spaces into account.

  Close

2010

• Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M :
  Flexible Experimentation in the Modeling and Simulation Framework JAMES II --- Implications for Computational Systems Biology.
  Briefings in Bioinformatics 11 (3)
  [view online] [abstract] [bibtex]
  ×
  

  Flexible Experimentation in the Modeling and Simulation Framework JAMES II --- Implications for Computational Systems Biology

                                      
  @article{Ewald2010,
  author = {Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M}, 
  year = {2010}, 
  title = {Flexible Experimentation in the Modeling and Simulation Framework
  JAMES II --- Implications for Computational Systems Biology}, 
  pages = {290--300}, 
  journal = {Briefings in Bioinformatics}, 
  volume = {11}, 
  number = {3}, 
  }
  

  Close
  ×
  

  Flexible Experimentation in the Modeling and Simulation Framework JAMES II --- Implications for Computational Systems Biology

  Dry-lab experimentation is increasingly used to complement wet-lab experimentation. However, conducting dry-lab experiments is a challenging endeavor that requires the combination of diverse techniques. JAMES II, a plug-in based open source modeling and simulation framework, facilitates the exploitation and configuration of these techniques. The different aspects that form an experiment are made explicit to facilitate repeatability and reuse. Each of those influences the performance and the quality of the simulation experiment. Common experimentation pitfalls and current challenges are discussed along the way.

  Close
• Ewald, Roland and Schulz, René and Uhrmacher, Adelinde M :
  Selecting Simulation Algorithm Portfolios by Genetic Algorithms.
  IEEE Workshop on Principles of Advanced and Distributed Simulation (PADS)
  [view online] [abstract] [bibtex]
  ×
  

  Selecting Simulation Algorithm Portfolios by Genetic Algorithms

                                      
  @inproceedings{Ewald2010a,
  author = {Ewald, Roland and Schulz, René and Uhrmacher, Adelinde M}, 
  year = {2010}, 
  title = {Selecting Simulation Algorithm Portfolios by Genetic Algorithms}, 
  booktitle = {IEEE Workshop on Principles of Advanced and Distributed Simulation
  (PADS)}, 
  pages = {48--56}, 
  publisher = {IEEE CPS}, 
  }
  

  Close
  ×
  

  Selecting Simulation Algorithm Portfolios by Genetic Algorithms

  An algorithm portfolio is a set of algorithms that are bundled together for increased overall performance. While being mostly applied to computationally hard problems so far, we investigate portfolio selection for simulation algorithms and focus on their application to adaptive simulation replication. Since the portfolio selection problem is itself hard to solve, we introduce a genetic algorithm to select the most promising portfolios from large sets of simulation algorithms. The effectiveness of this mechanism is evaluated by data from both a realistic performance study and a dedicated test environment.

  Close
• Himmelspach, Jan and Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M :
  Enhancing the Scalability of Simulations by Embracing Multiple Levels of Parallelization.
  Proceedings of the 2010 International Workshop on High Performance Computational Systems Biology
  [view online] [abstract] [bibtex]
  ×
  

  Enhancing the Scalability of Simulations by Embracing Multiple Levels of Parallelization

                                      
  @inproceedings{Himmelspach2010,
  author = {Himmelspach, Jan and Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M}, 
  year = {2010}, 
  title = {Enhancing the Scalability of Simulations by Embracing Multiple Levels
  of Parallelization}, 
  booktitle = {Proceedings of the 2010 International Workshop on High Performance
  Computational Systems Biology}, 
  publisher = {IEEE CPS}, 
  }
  

  Close
  ×
  

  Enhancing the Scalability of Simulations by Embracing Multiple Levels of Parallelization

  Current and upcoming architectures of desktop and high performance computers offer increasing means for parallel execution. Since the computational demands induced by ever more realistic models increase steadily, this trend is of growing importance for systems biology. Simulations of these models may involve the consideration of multiple parameter combinations, their replications, data collection, and data analysis—all of which offer different opportunities for parallelization. We present a brief theoretical analysis of these opportunities in order to show their potential impact on the overall computation time. The benefits of using more than one opportunity for parallelization are illustrated by a set of benchmark experiments, which furthermore show that parallelizability should be exploited in a flexible manner to achieve speedup.

  Close
• Uhrmacher, Adelinde M. and Himmelspach, Jan and Ewald, Roland :
  Effective and Efficient Modeling and Simulation with DEVS Variants.
  Discrete-Event Modeling and Simulation: Theory and Applications Book Chapter
  [view online] [bibtex]
  ×
  

  Effective and Efficient Modeling and Simulation with DEVS Variants

                                      
  @incollection{Uhrmacher2010,
  author = {Uhrmacher, Adelinde M. and Himmelspach, Jan and Ewald, Roland}, 
  year = {2010}, 
  title = {Effective and Efficient Modeling and Simulation with DEVS Variants}, 
  booktitle = {Discrete-Event Modeling and Simulation: Theory and Applications}, 
  publisher = {Taylor and Francis}, 
  editor = {G. Wainer and P. Mosterman}, 
  note = {Book Chapter}, 
  }
  

  Close
  ×
  

  Effective and Efficient Modeling and Simulation with DEVS Variants

  Close

2009

• Bohk, Christina and Ewald, Roland and Uhrmacher, Adelinde M. :
  Probabilistic Population Projection with James II.
  Proceedings of the 2009 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  Probabilistic Population Projection with James II

                                      
  @inproceedings{Bohk2009,
  author = {Bohk, Christina and Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2009}, 
  title = {Probabilistic Population Projection with James II}, 
  booktitle = {Proceedings of the 2009 Winter Simulation Conference}, 
  pages = {2008--2019}, 
  publisher = {IEEE Computer Science}, 
  editor = {Rossetti, M. D. and Hill, R. R. and Johansson, B. and Dunkin, A.
  and Ingalls, R. G.}, 
  doi = {http://dx.doi.org/10.1109/WSC.2009.5429715}, }
  

  Close
  ×
  

  Probabilistic Population Projection with James II

  Predicting future populations and their structure is a central theme in demography. It is related to public health issues, political decision-making, or urban planning. Since these predictions are concerned with the evolution of a complex system, they exhibit a considerable uncertainty. Accounting for this inherent uncertainty is crucial for subsequent decision processes, as it reveals the range of possible outcomes and their likelihood. Consequently, probabilistic prediction approaches emerged over the past decades. This paper describes the probabilistic population projection model (PPPM), a recently developed method that allows detailed projections, but has a complex structure and requires much input data. We discuss the development of P3J, a tool that helps users in managing and executing projections and is built on top of the simulation system JAMES II. We outline how even specific tools like P3J profit from general-purpose simulation frameworks like JAMES II, and illustrate its usage by a simple example.

  Close
• Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M :
  Performance Issues in Evaluating Models and Designing Simulation Algorithms.
  Proceedings of the 2009 International Workshop on High Performance Computational Systems Biology
  [view online] [abstract] [bibtex]
  ×
  

  Performance Issues in Evaluating Models and Designing Simulation Algorithms

                                      
  @inproceedings{Ewald2009b,
  author = {Ewald, Roland and Himmelspach, Jan and Jeschke, Matthias and Leye, Stefan and Uhrmacher, Adelinde M}, 
  year = {2009}, 
  title = {Performance Issues in Evaluating Models and Designing Simulation
  Algorithms}, 
  booktitle = {Proceedings of the 2009 International Workshop on High Performance
  Computational Systems Biology}, 
  pages = {71-80}, 
  publisher = {IEEE CPS}, 
  }
  

  Close
  ×
  

  Performance Issues in Evaluating Models and Designing Simulation Algorithms

  The increase and diversity of simulation methods bears witness of the need for more efficient discrete event simulations in computational biology --- but how efficient are those methods, and how to ensure an efficient simulation for a concrete model? As the performance of simulation methods depends on the model, the simulator, and the infrastructure, general answers to those questions are likely to remain illusive; they have to be sought individually and experimentally instead. This requires configurable implementations of many algorithms, means to define and conduct meaningful experiments on them, and mechanisms for storing and analyzing observed performance data. In this paper, we first overview basic approaches for improving simulation performance and illustrate the challenges when comparing different methods. We then argue that providing all the aforementioned components in a single tool, in our case the open source modeling and simulation framework JAMES II, reveals many synergies in effectively pursuing both questions. This is exemplified by presenting results of recent studies and introducing a new component to swiftly evaluate simulator code changes against previous experimental data.

  Close
• Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M :
  An Efficient and Adaptive Mechanism for Parallel Simulation Replication.
  Proceedings of the 23rd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS)
  [view online] [abstract] [bibtex]
  ×
  

  An Efficient and Adaptive Mechanism for Parallel Simulation Replication

                                      
  @inproceedings{Ewald2009a,
  author = {Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M}, 
  year = {2009}, 
  title = {An Efficient and Adaptive Mechanism for Parallel Simulation Replication}, 
  booktitle = {Proceedings of the 23rd ACM/IEEE/SCS Workshop on Principles of Advanced
  and Distributed Simulation (PADS)}, 
  pages = {104-113}, 
  publisher = {IEEE Conference Publishing Services}, 
  }
  

  Close
  ×
  

  An Efficient and Adaptive Mechanism for Parallel Simulation Replication

  Simulation replication is a necessity for all stochastic simulations. Its efficient execution is particularly important when additional techniques are used on top, such as optimization or sensitivity analysis. One way to improve replication efficiency is to ensure that the best configuration of the simulation system is used for execution. A selection of the best configuration is possible when the number of required replications is sufficiently high, even without any prior knowledge on simulator performance or problem instance. We present an adaptive replication mechanism that combines portfolio theory with reinforcement learning: it adapts itself to the given problem instance at runtime and can be restricted to an efficient algorithm portfolio.

  Close
• Ewald, Roland and Uhrmacher, Adelinde and Saha, Kaustav :
  Data Mining for Simulation Algorithm Selection.
  Proceedings of the 2nd International Conference on Simulation Tools and Techniques (SIMUTools)
  [view online] [abstract] [bibtex]
  ×
  

  Data Mining for Simulation Algorithm Selection

                                      
  @inproceedings{Ewald2009,
  author = {Ewald, Roland and Uhrmacher, Adelinde and Saha, Kaustav}, 
  year = {2009}, 
  title = {Data Mining for Simulation Algorithm Selection}, 
  booktitle = {Proceedings of the 2nd International Conference on Simulation Tools
  and Techniques (SIMUTools)}, 
  publisher = {ICST}, 
  doi = {http://dx.doi.org/%2010.4108/ICST.SIMUTOOLS2009.5659}, }
  

  Close
  ×
  

  Data Mining for Simulation Algorithm Selection

  While simulationists devise ever more efficient simulation algorithms for specific applications and infrastructures, the problem of automatically selecting the most appropriate one for a given problem has received little attention so far. One reason for this is the overwhelming amount of performance data that has to be analyzed for deriving suitable selection mechanisms. We address this problem with a framework for data mining on simulation performance data, which enables the evaluation of various data mining methods in this context. Such an evaluation is essential, as there is no best data mining algorithm for all kinds of simulation performance data. Once an effective data mining approach has been identified for a specific class of problems, its results can be used to select efficient algorithms for future simulation problems. This paper covers the components of the framework, the integration of external tools, and the re-formulation of the algorithm selection problem from a data mining perspective. Basic data mining strategies for algorithm selection are outlined, and a sample algorithm selection problem from Computational Biology is presented.

  Close
• Ewald, Roland and Uhrmacher, Adelinde M. :
  Automating the Runtime Performance Evaluation of Simulation Algorithms.
  Proceedings of the 2009 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  Automating the Runtime Performance Evaluation of Simulation Algorithms

                                      
  @inproceedings{Ewald2009c,
  author = {Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2009}, 
  title = {Automating the Runtime Performance Evaluation of Simulation Algorithms}, 
  booktitle = {Proceedings of the 2009 Winter Simulation Conference}, 
  pages = {1079--1091}, 
  publisher = {IEEE Computer Society}, 
  editor = {Rossetti, M. D. and Hill, R. R. and Johansson, B. and Dunkin, A.
  and Ingalls, R. G.}, 
  }
  

  Close
  ×
  

  Automating the Runtime Performance Evaluation of Simulation Algorithms

  Simulation algorithm implementations are usually evaluated by experimental performance analysis. To conduct such studies is a challenging and time-consuming task, as various impact factors have to be controlled and the resulting algorithm performance needs to be analyzed. This problem is aggravated when it comes to comparing many alternative implementations for a multitude of benchmark model setups. We present an architecture that supports the automated execution of performance evaluation experiments on several levels. Desirable benchmark model properties are motivated, and the quasi-steady state property of such models is exploited for simulation end time calibration, a simple technique to save computational effort in simulator performance comparisons. The overall mechanism is quite flexible and can be easily adapted to the various requirements that different kinds of performance studies impose. It is able to speed up performance experiments significantly, which is shown by a simple performance study.

  Close
• Theodoropoulos, Georgios and Minson, Rob and Ewald, Roland and Lees, Michael :
  Simulation Engines for Multi-Agent Systems.
  Agents, Simulation and Applications Book Chapter
  [view online] [bibtex]
  ×
  

  Simulation Engines for Multi-Agent Systems

                                      
  @incollection{Theodoropoulos2009,
  author = {Theodoropoulos, Georgios and Minson, Rob and Ewald, Roland and Lees, Michael}, 
  year = {2009}, 
  title = {Simulation Engines for Multi-Agent Systems}, 
  booktitle = {Agents, Simulation and Applications}, 
  pages = {77--105}, 
  publisher = {Taylor and Francis}, 
  editor = {Weyns, Danny and Uhrmacher, Adelinde M.}, 
  series = {Computational analysis, synthesis, and design of dynamic models}, 
  note = {Book Chapter}, 
  }
  

  Close
  ×
  

  Simulation Engines for Multi-Agent Systems

  Close
• Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping and Uhrmacher, Adelinde M. :
  Experimental Analysis of Logical Process Simulation Algorithms in JAMES II.
  Proceedings of the 2009 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  Experimental Analysis of Logical Process Simulation Algorithms in JAMES II

                                      
  @inproceedings{Wang2009,
  author = {Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping
  and Uhrmacher, Adelinde M.}, 
  year = {2009}, 
  title = {Experimental Analysis of Logical Process Simulation Algorithms in
  JAMES II}, 
  booktitle = {Proceedings of the 2009 Winter Simulation Conference}, 
  pages = {1167--1179}, 
  publisher = {IEEE Computer Science}, 
  editor = {Rossetti, M. D. and Hill, R. R. and Johansson, B. and Dunkin, A.
  and Ingalls, R. G.}, 
  doi = {http://dx.doi.org/10.1109/WSC.2009.5429633}, }
  

  Close
  ×
  

  Experimental Analysis of Logical Process Simulation Algorithms in JAMES II

  The notion of logical processes is a widely used modeling paradigm in parallel and distributed discrete-event simulation. Yet, the comparison among different simulation algorithms for LP models still remains difficult. Most simulation systems only provide a small subset of available algorithms, which are usually selected and tuned towards specific applications. Furthermore, many modeling and simulation frameworks blur the boundary between model logic and simulation algorithm, which hampers the extensibility and the comparability. Based on the general-purpose modeling and simulation framework JAMES II, which has already been used for experiments with algorithms several times, we present an environment for the experimental analysis of simulation algorithms for logical processes. It separates model from simulator concepts, is extensible (in regards to the benchmark models, the algorithms used, etc.), and facilitates a fair comparison of algorithms.

  Close
• Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping and Uhrmacher, Adelinde M :
  An Experimental Analysis Environment for Logical Process Simulation Algorithms.
  Proceedings of the 2nd International ICST Conference on Simulation Tools and Techniques (SIMUTools) Poster
  [view online] [abstract] [bibtex]
  ×
  

  An Experimental Analysis Environment for Logical Process Simulation Algorithms

                                      
  @misc{Wang2009Poster,
  author = {Wang, Bing and Himmelspach, Jan and Ewald, Roland and Yao, Yiping
  and Uhrmacher, Adelinde M}, 
  year = {2009}, 
  title = {An Experimental Analysis Environment for Logical Process Simulation
  Algorithms}, 
  booktitle = {Proceedings of the 2nd International ICST Conference on Simulation
  Tools and Techniques (SIMUTools)}, 
  note = {Poster}, 
  }
  

  Close
  ×
  

  An Experimental Analysis Environment for Logical Process Simulation Algorithms

  The notion of logical processes (LPs) is a widely used modeling paradigm in parallel and distributed discrete-event simulation (PDES). Nevertheless the comparison among different simulation algorithms for LP models still remains difficult: there are too many combinations of algorithms to be explored, often simulation systems only provide a small subset of available algorithms, and many m\&s frameworks blur the boundary between model logic and simulation algorithm, which hampers extensibility and comparability. We present an environment for the experimental analysis of simulation algorithms for logical processes. It separates between model and simulator, is extensible, and facilitates a fair comparison of algorithms. We illustrate the functioning of the environment by presenting experimental results for well-known simulation algorithms and a benchmark model.

  Close

2008

• Chen, Dan and Ewald, Roland and Theodoropoulos, Georgios K. and Minson, Robert and Oguara, Ton and Lees, Michael and Logan, Brian and Uhrmacher, Adelinde M. :
  Data Access in Distributed Simulations of Multi-agent Systems.
  Journal of Systems and Software 81 (12)
  [view online] [abstract] [bibtex]
  ×
  

  Data Access in Distributed Simulations of Multi-agent Systems

                                      
  @article{Chen2008,
  author = {Chen, Dan and Ewald, Roland and Theodoropoulos, Georgios K. and Minson, Robert and Oguara, Ton and Lees, Michael and Logan, Brian and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {Data Access in Distributed Simulations of Multi-agent Systems}, 
  pages = {2345--2360}, 
  journal = {Journal of Systems and Software}, 
  volume = {81}, 
  number = {12}, 
  doi = {10.1016/j.jss.2008.04.041}, }
  

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  ×
  

  Data Access in Distributed Simulations of Multi-agent Systems

  Distributed simulation has emerged as an important instrument for studying large-scale complex systems. Such systems inherently consist of a large number of components, which operate in a large shared state space interacting with it in highly dynamic and unpredictable ways. Optimising access to the shared state space is crucial for achieving efficient simulation executions. Data accesses may take two forms: locating data according to a set of attribute value ranges (range query) or locating a particular state variable from the given identifier (ID query and update). This paper proposes two alternative routing approaches, namely the address-based approach, which locates data according to their address information, and the range-based approach, whose operation is based on looking up attribute value range information along the paths to the destinations. The two algorithms are discussed and analysed in the context of PDES-MAS, a framework for the distributed simulation of multi-agent systems, which uses a hierarchical infrastructure to manage the shared state space. The paper introduces a generic meta-simulation framework which is used to perform a quantitative comparative analysis of the proposed algorithms under various circumstances.

  Close
• Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M. :
  An Algorithm Selection Approach for Simulation Systems.
  Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS)
  [view online] [abstract] [bibtex]
  ×
  

  An Algorithm Selection Approach for Simulation Systems

                                      
  @inproceedings{Ewald2008,
  author = {Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {An Algorithm Selection Approach for Simulation Systems}, 
  booktitle = {Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced
  and Distributed Simulation (PADS)}, 
  pages = {91--98}, 
  publisher = {IEEE Computer Society}, 
  volume = {22}, 
  doi = {10.1109/PADS.2008.9}, }
  

  Close
  ×
  

  An Algorithm Selection Approach for Simulation Systems

  No simulation algorithm will deliver best performance under all circumstances, so simulation systems often offer execution alternatives to choose from. This leads to another problem: how is the user supposed to know which algorithm to select? The need for an automated selection mechanism is often neglected, as many simulation systems are focused on specific applications or modeling formalisms and therefore have a limited number of expert users. In general-purpose simulation systems like JAMES II, an 'intelligent' selection mechanism could help to increase the overall performance, especially when users have limited knowledge of the underlying algorithms and their implementation(s)(which is almost always the case). We describe an approach to integrate algorithm selection methods with such systems. Its effectiveness is illustrated in conjunction with the 'plug 'n simulate' approach of JAMES II.

  Close
• Ewald, Roland and Rössel, Johannes and Himmelspach, Jan and Uhrmacher, Adelinde M. :
  A Plug-in-based Architecture for Random Number Generation in Simulation Systems.
  Proceedings of the 2008 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  A Plug-in-based Architecture for Random Number Generation in Simulation Systems

                                      
  @inproceedings{Ewald2008a,
  author = {Ewald, Roland and Rössel, Johannes and Himmelspach, Jan and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {A Plug-in-based Architecture for Random Number Generation in Simulation
  Systems}, 
  booktitle = {Proceedings of the 2008 Winter Simulation Conference}, 
  pages = {836-844}, 
  publisher = {IEEE Computer Society}, 
  editor = {Mason, S. J. and Hill, R. R. and Moench, L. and Rose, O.}, 
  doi = {10.1109/WSC.2008.4736147}, }
  

  Close
  ×
  

  A Plug-in-based Architecture for Random Number Generation in Simulation Systems

  Simulations often depend heavily on random numbers, yet the impact of random number generators is recognized seldom. The generation of random numbers for simulations is not trivial, as the quality of each algorithm depends on the simulation scenario. Therefore, simulation environments for large-scale experimentation with safety-critical models require a reliable mechanism to cope with this aspect. We show how to address this problem by realizing a random number generation architecture for a general-purpose simulation system. It provides various random number generators (RNGs), probability distributions, and RNG tests. It is open to future additions, which allows the assessment of new generators in a simulation context and the re-validation of past simulation studies. We present a short example that illustrates why the features of such an architecture are essential for getting valid results.

  Close
• Himmelspach, Jan and Ewald, Roland and Uhrmacher, Adelinde M :
  A Flexible and Scalable Experimentation Layer.
  Proceedings of the 2008 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  A Flexible and Scalable Experimentation Layer

                                      
  @inproceedings{Himmelspach2008,
  author = {Himmelspach, Jan and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2008}, 
  title = {A Flexible and Scalable Experimentation Layer}, 
  booktitle = {Proceedings of the 2008 Winter Simulation Conference}, 
  editor = {S.J. Mason and R.R. Hill and L. Moench and O. Rose}, 
  doi = {http://dx.doi.org/10.1109/WSC.2008.4736146}, }
  

  Close
  ×
  

  A Flexible and Scalable Experimentation Layer

  Modeling and simulation frameworks for use in different application domains, throughout the complete development process, and in different hardware environments need to be highly scalable. For achieving an efficient execution, different simulation algorithms and data structures must be provided to compute a concrete model on a concrete platform efficiently. The support of parallel simulation techniques becomes increasingly important in this context, which is due to the growing availability of multi-core processors and network-based computers. This leads to more complex simulation systems that are harder to configure correctly. We present an experimentation layer for the modeling and simulation framework JAMES II. It greatly facilitates the configuration and usage of the system for a user and supports distributed optimization, on-demand observation, and various distributed and non-distributed scenarios.

  Close
• Himmelspach, Jan and Röhl, Mathias and Ewald, Roland and Uhrmacher, Adelinde M :
  Plug'n Simulate: Scalability as a Key Requirement for SOA-based M&S?.
  Workshop on Net-Centric M&S Position Paper
  [bibtex]
  ×
  

  Plug'n Simulate: Scalability as a Key Requirement for SOA-based M&S?

                                      
  @misc{Himmelspach2008a,
  author = {Himmelspach, Jan and Röhl, Mathias and Ewald, Roland and Uhrmacher, Adelinde M}, 
  year = {2008}, 
  title = {Plug'n Simulate: Scalability as a Key Requirement for SOA-based M&S?}, 
  booktitle = {Workshop on Net-Centric M&S}, 
  note = {Position Paper}, 
  }
  

  Close
  ×
  

  Plug'n Simulate: Scalability as a Key Requirement for SOA-based M&S?

  Close
• Jeschke, Matthias and Ewald, Roland :
  Large-Scale Design Space Exploration of SSA.
  Computational Methods in Systems Biology (CMSB 2008)
  [view online] [abstract] [bibtex]
  ×
  

  Large-Scale Design Space Exploration of SSA

                                      
  @inproceedings{Jeschke2008c,
  author = {Jeschke, Matthias and Ewald, Roland}, 
  year = {2008}, 
  title = {Large-Scale Design Space Exploration of SSA}, 
  booktitle = {Computational Methods in Systems Biology (CMSB 2008)}, 
  pages = {211--230}, 
  publisher = {Springer Berlin / Heidelberg}, 
  volume = {5307}, 
  series = {Lecture Notes in Computer Science}, 
  doi = {10.1007/978-3-540-88562-7_17}, }
  

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  ×
  

  Large-Scale Design Space Exploration of SSA

  Stochastic simulation algorithms (SSA) are popular methods for the simulation of chemical reaction networks, so that various enhancements have been introduced and evaluated over the years. However, neither theoretical analysis nor empirical comparisons of single implementations suffice to capture the general performance of a method. This makes choosing an appropriate algorithm very hard for anyone who is not an expert in the field, especially if the system provides many alternative implementations. We argue that this problem can only be solved by thoroughly exploring the design spaces of such algorithms. This paper presents the results of an empirical study, which subsumes several thousand simulation runs. It aims at exploring the performance of different SSA implementations and comparing them to an approximation via tau-Leaping, while using different event queues and random number generators.

  Close
• Jeschke, Matthias and Ewald, Roland and Park, Alfred and Fujimoto, Richard and Uhrmacher, Adelinde M. :
  A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological Simulations.
  ACM SIGMETRICS Performance Evaluation Review 35 (4) Invited Paper
  [view online] [abstract] [bibtex]
  ×
  

  A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological Simulations

                                      
  @article{Jeschke2008a,
  author = {Jeschke, Matthias and Ewald, Roland and Park, Alfred and Fujimoto, Richard and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological
  Simulations}, 
  pages = {22--31}, 
  publisher = {ACM}, 
  journal = {ACM SIGMETRICS Performance Evaluation Review}, 
  volume = {35}, 
  number = {4}, 
  note = {Invited Paper}, 
  doi = {10.1145/1364644.1364652}, }
  

  Close
  ×
  

  A Parallel and Distributed Discrete Event Approach for Spatial Cell-Biological Simulations

  As data and knowledge about cell-biological systems increases so does the need for simulation tools to support a hypothesis driven wet-lab experimentation. Discrete event simulation has received a lot of attention lately, however, often its application is hampered by its lack of performance. One solution are parallel, distributed approaches, however, their application is limited by the amount of parallelism available in the model. Recent studies have shown that spatial aspects are crucial for cell biological dynamics and they are also a promising candidate to exploit parallelism. Promises and specific requirements imposed by a spatial simulation of cell biological systems will be illuminated by a parallel and distributed variant of the Next-Subvolume Method (NSM), which augments the Stochastic Simulation Algorithm (SSA) with spatial features, and its realization in a grid-inspired simulation system called Aurora.

  Close
• Jeschke, Matthias and Park, Alfred and Ewald, Roland and Fujimoto, Richard and Uhrmacher, Adelinde M. :
  Parallel and Distributed Spatial Simulation of Chemical Reactions.
  Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS)
  [view online] [abstract] [bibtex]
  ×
  

  Parallel and Distributed Spatial Simulation of Chemical Reactions

                                      
  @inproceedings{Jeschke2008d,
  author = {Jeschke, Matthias and Park, Alfred and Ewald, Roland and Fujimoto, Richard and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {Parallel and Distributed Spatial Simulation of Chemical Reactions}, 
  booktitle = {Proceedings of the 22nd ACM/IEEE/SCS Workshop on Principles of Advanced
  and Distributed Simulation (PADS)}, 
  pages = {51--59}, 
  publisher = {IEEE Computer Society}, 
  doi = {10.1109/PADS.2008.20}, }
  

  Close
  ×
  

  Parallel and Distributed Spatial Simulation of Chemical Reactions

  The application of parallel and distributed simulation techniques is often limited by the amount of parallelism available in the model. This holds true for large-scale cell-biological simulations, a field that has emerged as data and knowledge concerning these systems increases and biologists call for tools to guide wet-lab experimentation. A promising approach to exploit parallelism in this domain is the integration of spatial aspects, which are often crucial to a model's validity. We describe an optimistic, parallel and distributed variant of the Next-Subvolume Method (NSM), a method that augments the well-known Gillespie Stochastic Simulation Algorithm (SSA) with spatial features. We discuss requirements imposed by this application on a parallel discrete event simulation engine to achieve efficient execution. First results of combining NSM and the grid-inspired simulation system Aurora are shown.

  Close
• John, Mathias and Ewald, Roland and Uhrmacher, Adelinde M. :
  A Spatial Extension to the Pi-Calculus.
  Electronic Notes in Theoretical Computer Science 194 (3)
  [view online] [abstract] [bibtex]
  ×
  

  A Spatial Extension to the Pi-Calculus

                                      
  @article{John2008,
  author = {John, Mathias and Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {A Spatial Extension to the Pi-Calculus}, 
  pages = {133--148}, 
  journal = {Electronic Notes in Theoretical Computer Science}, 
  volume = {194}, 
  number = {3}, 
  doi = {10.1016/j.entcs.2007.12.010}, }
  

  Close
  ×
  

  A Spatial Extension to the Pi-Calculus

  Spatial dynamics receive increasing attention in Systems Biology and require suitable modeling and simulation approaches. So far, modeling formalisms have focused on population-based approaches or place and move individuals relative to each other in space. SpacePi extends the [pi] calculus by time and space. [pi] processes are embedded into a vector space and move individually. Only processes that are sufficiently close can communicate. The operational semantics of SpacePi defines the interplay between movement, communication, and time-triggered events. A model describing the phototaxis of the Euglena micro-organism is presented as a practical example. The formalism's use and generality is discussed with respect to the modeling of molecular biological processes like diffusion, active transportation in cell signaling, and spatial structures.

  Close
• Leye, Stefen and Himmelspach, Jan and Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M. :
  A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution.
  Proceedings of the 12th IEEE/ACM International Symposium on Distributed Simulation and Real-Time Applications (DS-RT)
  [view online] [abstract] [bibtex]
  ×
  

  A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution

                                      
  @inproceedings{Leye2008,
  author = {Leye, Stefen and Himmelspach, Jan and Jeschke, Matthias and Ewald, Roland and Uhrmacher, Adelinde M.}, 
  year = {2008}, 
  title = {A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution}, 
  booktitle = {Proceedings of the 12th IEEE/ACM International Symposium on Distributed
  Simulation and Real-Time Applications (DS-RT)}, 
  pages = {7--16}, 
  publisher = {IEEE Computer Society}, 
  doi = {10.1109/DS-RT.2008.33}, }
  

  Close
  ×
  

  A Grid-Inspired Mechanism for Coarse-Grained Experiment Execution

  Stochastic simulations may require many replications until their results are statistically significant. Each replication corresponds to a standalone simulation job, so that these can be computed in parallel. This paper presents a grid-inspired approach to distribute such independent jobsover a set of computing resources that host simulation services, all of which are managed by a central master service. Our method is fully integrated with alternative ways of distributed simulation in JAMES II, hides all execution details from the user, and supports the coarse-grained parallel execution of any sequential simulator available in JAMES II. A thorough performance analysis of the new execution mode illustrates its efficiency.

  Close
• Martens, Alke and Himmelspach, Jan and Ewald, Roland :
  Spiele und Simulation.
  Proceedings of the International Scientific E-Learning Baltics Conference
  [abstract] [bibtex]
  ×
  

  Spiele und Simulation

                                      
  @inproceedings{Martens2008a,
  author = {Martens, Alke and Himmelspach, Jan and Ewald, Roland}, 
  year = {2008}, 
  title = {Spiele und Simulation}, 
  booktitle = {Proceedings of the International Scientific E-Learning Baltics Conference}, 
  pages = {53-62}, 
  publisher = {Fraunhofer IRB Verlag}, 
  editor = {Hambach, S. and Martens, A. and Urban, B.}, 
  }
  

  Close
  ×
  

  Spiele und Simulation

  Modellbildung und Simulation sind schon seit langer Zeit Bestandteil der Entwicklung von Spielen, und auch von Game-based Learning Systemen. Im Gegensatz zu dieser langen Tradition steht die Tatsache, dass Forschungen in beiden Bereichen häufig parallel läuft. In Spielen wird häufig nicht expliziert, wie welche Modelle entwickelt wurden oder welche Simulationsalgorithmen verwendet werden. In Simulationssystemen werden oft Testszenarien entwickelt, die spielerischen Charakter haben, ohne das dies notwendiger Weise die Entwicklung von Game-based Learning oder von Spielen voran bringt. Da Forschung in Modellbildung und Simulation die Spielentwicklung voran bringen kann, und umgekehrt Spielszenarien interessante Testumgebungen für Experimente darstellen können, wird in diesem Papier der Ansatz gemacht, das Feld zu strukturieren. Dabei werden die drei Bereiche Modellbildung und Simulation, Spiele und Game-based Learning betrachtet.

  Close
• Martens, Alke and Himmelspach, Jan and Ewald, Roland :
  Modeling, Simulation and Games.
  Workshop Proceedings der Tagungen Mensch und Computer 2008, Delfi 2008 und Cognitive Design 2008
  [abstract] [bibtex]
  ×
  

  Modeling, Simulation and Games

                                      
  @inproceedings{Martens2008,
  author = {Martens, Alke and Himmelspach, Jan and Ewald, Roland}, 
  year = {2008}, 
  title = {Modeling, Simulation and Games}, 
  booktitle = {Workshop Proceedings der Tagungen Mensch und Computer 2008, Delfi
  2008 und Cognitive Design 2008}, 
  pages = {349--354}, 
  publisher = {Logos Verlag, Berlin}, 
  editor = {Lucke, U. and Kindsm{\"{u}}ller, M. C. and Fischer, S. and Herczeg, M. and Seehusen, S.}, 
  }
  

  Close
  ×
  

  Modeling, Simulation and Games

  Using modeling and simulation techniques in game development can look back on a comparably long history, starting in the early 1970s. In contrast to this long tradition of combining games and simulations, it is usually not made explicit which kind of simulation is used, which models are fundament of the simulation, and which role the simulation and the models have in the game based scenario (e.g. non-player characters, environment, engines). This has led to a situation where research in modeling and simulation and development of games run in parallel -- it is not clear how recent research results influence the interwoven development of both fields. This paper will start with an attempt to structure both fields, and to provide for a collection of defined terms, which help to relate modeling and simulation approaches to game development.

  Close
• Uhrmacher, Adelinde and Himmelspach, Jan and Jeschke, Matthias and John, Mathias and Leye, Stefan and Maus, Carsten and Röhl, Mathias and Ewald, Roland :
  One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II.
  Proceedings of the 1st International Workshop on Formal Methods in Systems Biology
  [view online] [abstract] [bibtex]
  ×
  

  One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II

                                      
  @incollection{Uhrmacher2008,
  author = {Uhrmacher, Adelinde and Himmelspach, Jan and Jeschke, Matthias and
  John, Mathias and Leye, Stefan and Maus, Carsten and Röhl, Mathias
  and Ewald, Roland}, 
  year = {2008}, 
  title = {One Modelling Formalism & Simulator Is Not Enough! A Perspective
  for Computational Biology Based on James II}, 
  booktitle = {Proceedings of the 1st International Workshop on Formal Methods in
  Systems Biology}, 
  pages = {123--138}, 
  publisher = {Springer Berlin / Heidelberg}, 
  series = {Lecture Notes in Bioinformatics}, 
  doi = {10.1007/978-3-540-68413-8_9}, }
  

  Close
  ×
  

  One Modelling Formalism & Simulator Is Not Enough! A Perspective for Computational Biology Based on James II

  Diverse modelling formalisms are applied in Computational Biology. Some describe the biological system in a continuous manner, others focus on discrete-event systems, or on a combination of continuous and discrete descriptions. Similarly, there are many simulators that support different formalisms and execution types (e.g. sequential, parallel-distributed) of one and the same model. The latter is often done to increase efficiency, sometimes at the cost of accuracy and level of detail. JAMES II has been developed to support different modelling formalisms and different simulators and their combinations. It is based on a plug-in concept which enables developers to integrate spatial and non-spatial modelling formalisms (e.g. Stochastic Pi, Beta Binders, DEVS, Space Pi), simulation algorithms (e.g. variants of Gillespie's algorithms (including Tau Leaping and NSM), Space Pi simulator, parallel Beta Binders simulator) and supporting technologies (e.g. partitioning algorithms, data collection mechanisms, data structures, random number generators) into an existing framework. This eases method development and result evaluation in applied modelling and simulation as well as in modelling and simulation research.

  Close

2007

• Ewald, Roland and Maus, Carsten and Rolfs, Arndt and Uhrmacher, Adelinde M. :
  Discrete Event Modeling and Simulation in Systems Biology.
  Journal of Simulation 1 (2)
  [view online] [abstract] [bibtex]
  ×
  

  Discrete Event Modeling and Simulation in Systems Biology

                                      
  @article{Ewald2007,
  author = {Ewald, Roland and Maus, Carsten and Rolfs, Arndt and Uhrmacher, Adelinde
  M.}, 
  year = {2007}, 
  title = {Discrete Event Modeling and Simulation in Systems Biology}, 
  pages = {81--96}, 
  journal = {Journal of Simulation}, 
  volume = {1}, 
  number = {2}, 
  doi = {10.1057/palgrave.jos.4250018}, }
  

  Close
  ×
  

  Discrete Event Modeling and Simulation in Systems Biology

  With Systems Biology, a promising new application area for modeling and simulation emerges. Today's biologists are facing huge amounts of data delivered at different levels of detail by a multitude of advanced experimentation techniques. The Systems Biology approach copes with this information by cycling through phases of forming hypothesis, constructing models, experimenting with or analyzing these models, and validating the findings by wet-lab experiments. A crucial point is therefore the way in which the knowledge about a system is formalized, i.e., how a biological system is described as this constrains the perception of the system as well as scope of possible answers the model might provide. In this article, we compare different discrete-event modeling formalisms (Petri Nets, Stochastic Pi-Calculus , StateCharts, and Devs) regarding their applicability to a cell biological system of current research interest, the Wnt signaling pathway. We then introduce the popular Gillespie algorithm, which is the foundation of many discrete-event simulators for molecular-biological systems, and elaborate on some interesting extensions.

  Close
• Himmelspach, Jan and Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M. :
  Parallel and Distributed Simulation of Parallel DEVS Models.
  Proceedings of the SpringSim '07, DEVS Integrative M&S Symposium
  [view online] [abstract] [bibtex]
  ×
  

  Parallel and Distributed Simulation of Parallel DEVS Models

                                      
  @inproceedings{Himmelspach2007b,
  author = {Himmelspach, Jan and Ewald, Roland and Leye, Stefan and Uhrmacher, Adelinde M.}, 
  year = {2007}, 
  title = {Parallel and Distributed Simulation of Parallel DEVS Models}, 
  booktitle = {Proceedings of the SpringSim '07, DEVS Integrative M&S Symposium}, 
  pages = {249--256}, 
  publisher = {SCS}, 
  }
  

  Close
  ×
  

  Parallel and Distributed Simulation of Parallel DEVS Models

  Distributed simulation can speed up the execution of models significantly. We introduce a new simulation algorithm and present partitioning and load balancing techniques that are tailored to the efficient distributed execution of PDEVS. We base our elaborations on the idea of minimizing inter-processor communication, since this is a major bottleneck in distributed PDEVS simulation. Additionally, experimental results are provided which compare the performance of this new approach to alternative algorithms.

  Close
• Uhrmacher, Adelinde M. and Ewald, Roland and John, Mathias and Maus, Carsten and Jeschke, Matthias and Biermann, Susanne :
  Combining Micro and Macro-Modeling in DEVS for Computational Biology.
  Proceedings of the 2007 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  Combining Micro and Macro-Modeling in DEVS for Computational Biology

                                      
  @inproceedings{Uhrmacher2007,
  author = {Uhrmacher, Adelinde M. and Ewald, Roland and John, Mathias and Maus, Carsten and Jeschke, Matthias and Biermann, Susanne}, 
  year = {2007}, 
  title = {Combining Micro and Macro-Modeling in DEVS for Computational Biology}, 
  booktitle = {Proceedings of the 2007 Winter Simulation Conference}, 
  pages = {871-880}, 
  publisher = {IEEE Press}, 
  doi = {10.1109/WSC.2007.4419683}, }
  

  Close
  ×
  

  Combining Micro and Macro-Modeling in DEVS for Computational Biology

  In computational biology there is an increasing need to combine micro and macro views of the system of interest. Therefore, explicit means to describe micro and macro level and the downward and upward causation that link both are required. Multi-Level-DEVS (or ml-DEVS) supports an explicit description of macro and micro level, information at macro level can be accessed from micro level and vice versa, micro models can be synchronously activated by the macro model and also the micro models can trigger the dynamics at macro level. To link both levels, different methods are combined, to those belong, value coupling, synchronous activations, variable ports, and invariants. The execution semantic of the formalism is given by an abstract simulator and its use is illustrated based on an small extract of the Wnt pathway.

  Close

2006

• Batt, Gregory and Bradley, Jeremy T. and Ewald, Roland and Fages, Francois and Hermans, Holger and Hillston, Jane and Kemper, Peter and Martens, Alke and Mosterman, Pieter and Nielson, Flemming and Sokolsky, Oleg and Uhrmacher, Adelinde M. :
  06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification.
  Simulation and Verification of Dynamic Systems, Dagstuhl Seminar Proceedings Report
  [view online] [bibtex]
  ×
  

  06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification

                                      
  @misc{Batt2006,
  author = {Batt, Gregory and Bradley, Jeremy T. and Ewald, Roland and Fages, Francois and Hermans, Holger and Hillston, Jane and Kemper, Peter
  and Martens, Alke and Mosterman, Pieter and Nielson, Flemming and
  Sokolsky, Oleg and Uhrmacher, Adelinde M.}, 
  year = {2006}, 
  title = {06161 Working Groups' Report: The Challlenge of Combining Simulation
  and Verification}, 
  booktitle = {Simulation and Verification of Dynamic Systems, Dagstuhl Seminar
  Proceedings}, 
  publisher = {Internationales Begegnungs- und Forschungszentrum für Informatik
  (IBFI), Schloss Dagstuhl, Germany}, 
  editor = {Nicol, David M. and Priami, Corrado and Nielson, Hanne R. and Uhrmacher, Adelinde M.}, 
  number = {06161}, 
  series = {Dagstuhl Seminar Proceedings}, 
  note = {Report}, 
  }
  

  Close
  ×
  

  06161 Working Groups' Report: The Challlenge of Combining Simulation and Verification

  Close
• Chen, Dan and Ewald, Roland and Theodoropoulos, Georgios K. and Oguara, Tonworio :
  Data Management in Distributed Simulation of Complex Systems.
  Technical Report CSR-06-06, University of Birmingham, School of Computer Science Report
  [preprint] [view online] [abstract] [bibtex]
  ×
  

  Data Management in Distributed Simulation of Complex Systems

                                      
  @techreport{Chen2006,
  author = {Chen, Dan and Ewald, Roland and Theodoropoulos, Georgios K. and Oguara, Tonworio}, 
  year = {2006}, 
  title = {Data Management in Distributed Simulation of Complex Systems}, 
  booktitle = {Technical Report CSR-06-06, University of Birmingham, School of Computer
  Science}, 
  number = {CSR-06-06}, 
  note = {Report}, 
  }
  

  Close
  ×
  

  Data Management in Distributed Simulation of Complex Systems

  Distributed simulation has emerged as an important instrument for studying large-scale complex systems. Such systems inherently consist of a large number of components, which operate in a large shared state space interacting with it in highly dynamic and unpredictable ways. Optimising access to the enormous shared data is crucial for achieving efficient simulation executions. This effort involves two major issues, data distribution and data accessing. In this paper, we discuss the issues of modelling shared data. We have developed a framework for distributed simulation of MAS, which uses a hierarchical infrastructure to manage the shared data and facilitate interoperation amongst agent simulation models. Our framework aims to reduce the cost of accessing shared data by dynamically redistributing shared data in the infrastructure according to the access pattern of the agent simulation models. Data accesses may take two forms: locating data according to a set of attribute value ranges (Range query) locating a particular state variable from the given identifier (ID query and update). This paper proposes two alternative routing approaches, namely the address-based approach, which locates data according to their address information, and the range-based approach, whose operation is based on looking up attribute value range information along the paths to the destinations. The two algorithms are discussed an analysed in the context of PDES-MAS, a framework for the distributed simulation of multi-agent systems, which uses a hierarchical infrastructure to manage the shared state space. The paper introduces a generic meta-simulation framework which is used to perform a quantitative comparative analysis of the proposed algorithms under various circumstances.

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• Ewald, Roland :
  Simulation of Load Balancing Algorithms for Discrete Event Simulations.
  Universität Rostock Diploma Thesis
  [preprint] [abstract] [bibtex]
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  Simulation of Load Balancing Algorithms for Discrete Event Simulations

                                      
  @mastersthesis{Ewald2006MSc,
  author = {Ewald, Roland}, 
  year = {2006}, 
  title = {Simulation of Load Balancing Algorithms for Discrete Event Simulations}, 
  booktitle = {Universität Rostock}, 
  note = {Diploma Thesis}, 
  }
  

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  Simulation of Load Balancing Algorithms for Discrete Event Simulations

  Efficiently simulating discrete-event models in a parallel and distributed manner is a challenging endeavour. On one hand, various factors, such as hardware infrastructure or model characteristics, have to be considered. On the other hand, there is a wide variety of algorithms which address ubproblems of parallel and distributed simulation and whose performance depends on the application at hand. This work illustrates the resulting difficulties with respect to the development of parallel and distributed simulation systems for general purposes. It is reasoned to what extent a prior analysis could facilitate this task. Approaches to predict the performance of parallel and distributed simulation systems are discussed. It is argued that the simulation of such a simulation system is a feasible approach. This claim is underpinned by implementing SimSim, a sequential simulator to simulate parallel and distributed simulation systems. Then, SimSim is used to develop a load balancing algorithm for the simulation of PDEVS models. The algorithm’s performance is analysed using SimSim. Finally, the predicted performance is compared to the real performance of the algorithm when running in the simulation system James II.

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• Ewald, Roland and Chen, Dan and Theodoropoulos, Georgios K. and Lees, Michael and Logan, Brian and Oguara, Ton and Uhrmacher, Adelinde M. :
  Performance Analysis of Shared Data Access Algorithms for Distributed Simulation of Multi-Agent Systems.
  Proceedings of the 20th ACM/IEEE/SCS Workshop on Principles of Advanced and Distributed Simulation (PADS)
  [view online] [abstract] [bibtex]
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  Performance Analysis of Shared Data Access Algorithms for Distributed Simulation of Multi-Agent Systems

                                      
  @inproceedings{Ewald2006,
  author = {Ewald, Roland and Chen, Dan and Theodoropoulos, Georgios K. and Lees, Michael and Logan, Brian and Oguara, Ton and Uhrmacher, Adelinde
  M.}, 
  year = {2006}, 
  title = {Performance Analysis of Shared Data Access Algorithms for Distributed
  Simulation of Multi-Agent Systems}, 
  booktitle = {Proceedings of the 20th ACM/IEEE/SCS Workshop on Principles of Advanced
  and Distributed Simulation (PADS)}, 
  doi = {10.1109/PADS.2006.29}, }
  

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  Performance Analysis of Shared Data Access Algorithms for Distributed Simulation of Multi-Agent Systems

  Distributed simulation is an important instrument for studying multi-agent systems (MAS). Such large scale MAS simulations often have a large shared state space. Moreover, the shared state and the access pattern of agent simulations both are highly dynamic and unpredictable. Optimising access to the shared data is crucial for achieving efficient simulation executions. PDES-MAS is a framework for distributed simulation of MAS, which uses a hierarchical infrastructure to manage the shared data. In order to enable agent simulations to access distributed shared data efficiently, this paper proposes two routing algorithms, namely the address-based routing and the range-based routing. The paper introduces a meta-simulation approach to evaluate the characteristics of both solutions and provides a quantitative comparative analysis of the proposed algorithms.

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• Ewald, Roland and Gutzeit, Enrico and Schwanke, Sebastian and Uhrmacher, Adelinde and Lange, Christian and Biermann, Susanne and Maus, Carsten :
  Multi-Level Modeling with DEVS - A Critical Inspection and Steps Towards a Feasible Approach.
  Proceedings of the 2006 Winter Simulation Conference Poster
  [view online] [abstract] [bibtex]
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  Multi-Level Modeling with DEVS - A Critical Inspection and Steps Towards a Feasible Approach

                                      
  @misc{Ewald2006d,
  author = {Ewald, Roland and Gutzeit, Enrico and Schwanke, Sebastian and Uhrmacher, Adelinde and Lange, Christian and Biermann, Susanne and Maus, Carsten}, 
  year = {2006}, 
  title = {Multi-Level Modeling with DEVS - A Critical Inspection and Steps
  Towards a Feasible Approach}, 
  booktitle = {Proceedings of the 2006 Winter Simulation Conference}, 
  note = {Poster}, 
  }
  

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  Multi-Level Modeling with DEVS - A Critical Inspection and Steps Towards a Feasible Approach

  Multi-level modeling means the description of systems at different abstraction levels. In Systems Biology, different abstraction levels that arise from considering parts of the system at macro (e.g., concentrations) and parts of the system at micro (e.g., individual) level are of particular interest. Many modelling formalisms allow the modular and hierarchical construction of models. Those have often been inspired by DEVS and its construction of hierarchical models via the coupling of other models, but this type of hierarchy does still not allow a direct description of multi-level models, as the composed model has no behavior or state of its own. In DEVS, like in other modeling formalisms, macro and micro models are constructured as modular entities interacting with each other, as if they were equal sub-models. While this approach enables the use of established formalisms, it inhibits a clear distinction between the levels of abstraction and therefore hampers reusability, clearness and expressiveness. To overcome these problems, coupled DEVS models have been enriched by newly introduced high-level models that serve as a representation of the macro-level. Our approach is based on the rhoDEVS modelling formalism, which already provides variables structures, ports, and multi-couplings as key features. As an additional feature, high-level models may completely determine their coupled model's external input and output ports and can filter all inputs and outputs. This enables us to translate macro- and micro-level events over multiple abstraction levels. Furthermore, this behaviour could be very useful for modeling membrane systems. We present the realization of this approach in James II and the individual-based simulation of the canonical Wnt-Pathway as a sample application, in which a high-level model implementing the Gillespie approach serves as a particle collision scheduler. Similarly, a high-level model could include differential equations, or any other approach to model high-level properties of the system at hand. With its ability to survey all structural activities going on at the micro-level and to directly affect individuals by scheduling own events, the upward and downward causation in biological systems is captured. Although it looks as if we left DEVS far behind with this extension, it can be shown that models based on the extended formalism are still equivalent to basic DEVS models. Hence, the DEVS advantages, like modular composition of models via coupling, are preserved. Our approach is feasible to model any number of abstraction levels and can be coupled to other DEVS extensions (including hybrid models). We hope it eases the development of spatial biological models, including membranes, compartments and multiple abstraction levels.

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• Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M. :
  A Non-Fragmenting Partitioning Algorithm for Hierarchical Models.
  Proceedings of the 2006 Winter Simulation Conference
  [view online] [abstract] [bibtex]
  ×
  

  A Non-Fragmenting Partitioning Algorithm for Hierarchical Models

                                      
  @inproceedings{Ewald2006b,
  author = {Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M.}, 
  year = {2006}, 
  title = {A Non-Fragmenting Partitioning Algorithm for Hierarchical Models}, 
  booktitle = {Proceedings of the 2006 Winter Simulation Conference}, 
  pages = {848--855}, 
  publisher = {Winter Simulation Conference}, 
  }
  

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  A Non-Fragmenting Partitioning Algorithm for Hierarchical Models

  The simulation system James II is aimed at supporting a range of modeling formalisms and simulation engines. The partitioning of models is essential for distributed simulation. A suitable partition depends on model, hardware, and simulation algorithm characteristics. Therefore, a partitioning layer has been created in James II which allows to plug in partitioning algorithms on demand. Three different partitioning algorithms have been implemented. In addition to the well known Kernighan-Lin algorithm and a geometric approach, a partitioning algorithm for hierarchically structured models has been developed whose performance is evaluated.

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• Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M. and Chen, Dan and Theodoropoulos, Georgios K. :
  A Simulation Approach to Facilitate Parallel and Distributed Discrete-Event Simulator Development.
  Proceedings of the 10th IEEE International Symposium on Distributed Simulation and Real Time Applications (DS-RT)
  [view online] [abstract] [bibtex]
  ×
  

  A Simulation Approach to Facilitate Parallel and Distributed Discrete-Event Simulator Development

                                      
  @inproceedings{Ewald2006c,
  author = {Ewald, Roland and Himmelspach, Jan and Uhrmacher, Adelinde M. and
  Chen, Dan and Theodoropoulos, Georgios K.}, 
  year = {2006}, 
  title = {A Simulation Approach to Facilitate Parallel and Distributed Discrete-Event
  Simulator Development}, 
  booktitle = {Proceedings of the 10th IEEE International Symposium on Distributed
  Simulation and Real Time Applications (DS-RT)}, 
  pages = {209--218}, 
  publisher = {IEEE Computer Society}, 
  doi = {10.1109/DS-RT.2006.5}, }
  

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  ×
  

  A Simulation Approach to Facilitate Parallel and Distributed Discrete-Event Simulator Development

  Efficiently simulating discrete-event models in a parallel and distributed manner is a challenging endeavour. On one hand, various factors, such as hardware infrastructure or model characteristics, have to be considered. On the other hand, there is a wide variety of algorithms which address subproblems of parallel and distributed simulation and whose performance depends on the application at hand. We illustrate the resulting difficulties with respect to the development of parallel and distributed simulation systems and argue that the simulation of distributed simulation systems is a feasible approach to alleviate them. To illustrate this, we introduce SimSim, a sequential simulator that allows the simulation of parallel and distributed simulation systems. SimSim was used to develop a load balancing algorithm for the simulation of PDEVS models. The algorithm's performance is analysed using SimSim and the predicted performance is compared to the performance of its implementation in the simulation system James II.

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• Uhrmacher, Adelinde M. and Himmelspach, Jan and Röhl, Mathias and Ewald, Roland :
  Introducing Variable Ports and Multi-Couplings for Cell Biological Modeling in DEVS.
  Proceedings of the 2006 Winter Simulation Conference
  [view online] [abstract] [bibtex]
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  Introducing Variable Ports and Multi-Couplings for Cell Biological Modeling in DEVS

                                      
  @inproceedings{Uhrmacher2006,
  author = {Uhrmacher, Adelinde M. and Himmelspach, Jan and Röhl, Mathias and
  Ewald, Roland}, 
  year = {2006}, 
  title = {Introducing Variable Ports and Multi-Couplings for Cell Biological
  Modeling in DEVS}, 
  booktitle = {Proceedings of the 2006 Winter Simulation Conference}, 
  pages = {832-840}, 
  publisher = {IEEE Computer Society}, 
  editor = {L. F. Perrone and F. P. Wieland and J. Liu and B. G. Lawson and D.
  M. Nicol and R. M. Fujimoto}, 
  }
  

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  Introducing Variable Ports and Multi-Couplings for Cell Biological Modeling in DEVS

  Motivated by the requirements of molecular biological applications we are suggesting an extension of the {D}evs formalism. {S}tarting with dyn{D}evs a reflective variant of {D}evs which supports dynamic behavior, composition, and interaction pattern, we develop rho-{D}evs. {D}ynamic ports and multi-couplings are introduced whose combination allows models to reflect significant state changes to the outside world and enabling or disabling certain interactions at the same time. {A}n abstract simulator describes the operational semantics of the developed formalism, and the trp operon model illustrates the developed ideas and concepts.

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2005

• Ewald, Roland :
  Modellpartitionierung in JAMES II.
  Universität Rostock Student's Project
  [preprint] [abstract] [bibtex]
  ×
  

  Modellpartitionierung in JAMES II

                                      
  @misc{Ewald2005Studienarbeit,
  author = {Ewald, Roland}, 
  year = {2005}, 
  title = {Modellpartitionierung in JAMES II}, 
  booktitle = {Universität Rostock}, 
  note = {Student's Project}, 
  }
  

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  Modellpartitionierung in JAMES II

  Modellpartitionierung, also die Zerlegung eines Modells in verschiedene Teile, ist eine grundlegende Voraussetzung für die parallel-verteilte Ausführung von Simulationen. Zur Unterstützung dieser Funktionalität wird ein Framework zur Partitionierung in JAMES II integriert. Anschliessend wird ein Partitionierungsalgorithmus für DEVS-Modelle entwickelt und getestet.

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