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The Paper "An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers" has been accepted

The paper  "An explicit numerical scheme to efficiently simulate molecular diffusion in environments with dynamically changing barriers" by Christina Kossow, Stefan Rybacki, Thomas Millat, Katja Rateitschak,  Adelinde M. Uhrmacher  and Olaf Wolkenhauer has been accepted in the  journal Mathematical and Computer Modelling of Dynamical Systems

The Paper "Lattice Monte Carlo simulation of Galilei variant anomalous diffusion" has been accepted.

The paper "Lattice Monte Carlo simulation of Galilei variant anomalous diffusion" by Guo Gang,Bin Chen,Arne Bittig, Adelinde M. Uhrmacher has been accepted and published in the Journal of Computational Physics.

MOSI in Dagstuhl

MOSI members attended seminar "Multiscale Spatial Computational Systems Biology" in Dagstuhl.

On November 23 - 28, 2014, seminar "Multiscale Spatial Computational Systems Biology" was held in Dagstuhl, Germany. As one of the organizers, Prof. Adelinde M. Uhrmacher attended the seminar. MOSI member Arne Bittig, Sebastian Nähring and MOSI alumnus Carsten Maus were present.

For more detail, please see

MOSI in Manchester

MOSI members attended the conference CMSB in Manchester.

On 17-19 November 2014, four members of MOSI group attended CMSB 2014 (the 12th Conference on Computational Methods in Systems Biology) in Manchester, UK. Arne Bittig, Sebastian Nähring and Tom Warnke presented their posters. As a member of programme committee of the conference, Prof. Adelinde M. Uhrmacher was present as well.

JAMES II 0.9.6 Release

maintenance, moved DEVS project to bitbucket
  • DEVS: Moved DEVS to bitbucket
  • DEVS: Added simple examples (models) for basic DEVS
  • DEVS: Fixed some bugs in two basic DEVS simulators (flatsequential and abstractsequential)
  • CA: Fixed an NPE within the CA simulator
  • ML-Rules: Improved the parser to support negative attribute values

See for more details.

The Paper "Composing Problem Solvers for Simulation Experimentation: A Case Study on Steady State Estimation" has been accepted

The Artikel by Stefan Leye, Roland Ewald und Adelinde M. Uhrmacher will appear in PLOS ONE



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.

Researcher from China visits our Group

Dr. Eng Gang Guo visits the group for one year.

The modeling and simulation group welcomes the guest researcher Dr. Eng. Gang Guo from the NUDT (National University of Defense Technology, China) at our group. He already started his work at our group at the end of last year and he will stay until November, 2014. During this period, he will dedicate to parallel simulation of biological diffusion-reaction models on GPUs in collaboration with our group. The whole group wishes him a pleasant stay in Germany and we look forward to a successful cooperation.

Stefan Leye successfully completed his PhD

Congratulations, Stefan Leye successfully completed his PhD on "Toward Guiding Simulation Experiments".

JAMES II 0.9.4 Release

Improved and enhanced ML-DEVS simulator, maintenance
Major changes
  • ML-DEVS: added improved and enhanced version of the ML-DEVS simulator
Minor changes
  • Core: improved interface for simulation start and end hooks [JAMESII-427]
  • Result reporting: moved module 'resultreporting' to public repository [JAMESII-400]

See for more details.

The paper "SESSL: A Domain-Specific Language for Simulation Experiments" has been accepted for publication

The paper by Roland Ewald and Adelinde M. Uhrmacher will soon be published in the ACM Transactions on Modeling and Computer Simulation (TOMACS)


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.


Further details:


JAMES II 0.9.3 Release

New features: a generic adaptive simulator, SBML support for SR and ML-Rules, public code repository.

See for more details.

Proposal for Dagstuhl Seminar on Multiscale Spatial Computational Systems Biology Accepted

The proposal for a Dagstuhl Seminar on Multi-Scale Spatial Computational Systems Biology submitted by David Gilbert (Brunel University, UK), Monika Heiner (BTU Cottbus), Koichi Takahashi Riken, JP, and Adelinde M. Uhrmacher (University Rostock) has been accepted

The Dagstuhl Seminar on Multi-Scale Spatial Computational Systems Biology is scheduled for Monday, November 24 to Friday, November 28, 2014. More information about the seminar will soon be provided at the Dagstuhl web page

Release of the new website

Release of the new website which uses Plone 4

The previous website, which uses Plone 2 is replaced by the new website, which uses Plone 4. For visitors, most changes concern the design of the website. The content has not changed much. There is still information about our research, staff, and projects. Interested students also still find information about thesis topics, lectures and jobs.

Adelinde Uhrmacher editor in chief of TOMACS

Adelinde Uhrmacher is editor in chief of the ACM Transactions on Modeling and Computer Simulation.

The ACM Transactions on Modeling and Computer Simulation (TOMACS) is the premier international forum for research on discrete event stochastic modeling and simulation. In June 2013 Adelinde Uhrmacher became new editor in chief of the prestigious journal.

Paper on An Approximate Execution of Rule-based Multi-level Models accepted

The paper by Tobias Helms, Martin Luboschik, Heidrun Schumann, and Adelinde M. Uhrmacher will be presented within the CMSB 2013.

Abstract. In cell biology, models increasingly capture dynamics at different organizational levels. Therefore, new modeling languages are developed, e.g. like ML-Rules, that allow a compact and concise description of these models. However, the more complex models become the more important is an efficient execution of these models. τ-leaping algorithms can speed up the execution of biochemical reaction models significantly by introducing acceptable inaccurate results. Whereas those approximate algorithms appear particularly promising to be applied to hierarchically structured models, the dynamic nested structures cause specific challenges. We present a τ-leaping algorithm for ML-Rules which tackles these specific challenges and evaluate the efficiency and accuracy of this adapted τ-leaping based on a recently developed visual analysis technique.

New JAMES ii (0.9.2) release

A new official release of JAMES II is available for download now.
You can get your copy from here.

This is a beta release.

JAMES II is an open modeling and simulation framework based on a flexible, plug-in based architecture. In principal you should be able to use JAMES II as base for all your modeling and simulation jobs. The framework can be extended by any modeling formalism, simulation algorithm, and auxiliary algorithms required for the application of modeling and simulation, and for modeling and simulation research. It might be reused as is or you can integrate (parts of) the functionality JAMES II provides in your application.

Having published this release we start working on our additional (already existing) plug-ins to be able to release them as soon as possible as well.

We hope that you enjoy JAMES II, and we'd like to get any type of feedback. If you have questions don't hesitate to send us an e-mail.

The next release is scheduled for August 29, 2013.

Paper on Studying the role of lipid rafts on protein receptor bindings with Cellular Automata accepted

The paper by Fiete Haack, Kevin Burrage, Ronald Redmer, and Adelinde M. Uhrmacher will appear in IEEE/ACM Transactions on Computational Biology and Bioinformatics

Abstract—It is widely accepted that lipid rafts promote receptor clustering and thereby facilitate signalling transduction. The role of lipid rafts in inducing and promoting receptor accumulation within the cell membrane has been explored by several computational and experimental studies. However, it remains unclear whether lipid rafts influence the recruitment and binding of proteins from the cytosol as well. To provide an answer to this question a spatial membrane model has been developed based on cellular automata. Our results indicate that lipid rafts indeed influence protein receptor bindings. In particular processes with slow dissociation and binding kinetics are promoted by lipid rafts, whereas fast binding processes are slightly hampered. However, the impact depends on a variety of parameters, such as the size and mobility of the lipid rafts, the induced slow down of receptors within rafts, and also the dissociation and binding kinetics of the cytosolic proteins. Thus, for any individual signalling pathway the influence of lipid rafts on protein binding might be different. To facilitate analysing this influence given a specific pathway, our approach has been generalized into LiRaM, a modeling and simulation tool for Lipid Rafts Models.

DFG Contact Lecturer of the University of Rostock

Adelinde Uhrmacher is the DFG contact lecturer (German: "Vertrauensdozentin") of the University of Rostock since May the 1st, 2013.

Carsten Maus successfully finished his PhD

Towards Accessible Multilevel Modeling in Systems Biology

In March, Carsten Maus finished his PhD within GRK dIEM oSiRiS successfully. The faculty of computer science and electrical engineering of the University of Rostock confers the doctorate Dr.-Ing. on him for his dissertation "Towards Accessible Multilevel Modeling in Systems Biology".

We congratulate!

Adelinde M. Uhrmacher (University of Rostock, Germany), Ursual Krummer (University of Heidelberg, Germany), and James Faeder (University of Pittsburgh, USA) were the reviewers. Currently, Carsten Maus is working as a Post doctorand within the Group of Thomas Höfer at the University of Heidelberg.

The article "Membrane related dynamics and the formation of actin in cells growing on micro-topographies: A spatial computational model" has been published in BMC Systems Biology

A research paper by Arne T Bittig, Claudia Matschegewski, J. B Nebe, Susanne Stählke and Adelinde M Uhrmacher, a collaboration of the MoSi group and the Department of Cell Biology of the University Medical Center Rostock, has appeared in BMC Systems Biology.
DOI (link): 10.1186/s12918-014-0106-2. Abstract:

Background: Intra-cellular processes of cells at the interface to an implant surface are influenced significantly by their extra-cellular surrounding. Specifically, when growing osteoblasts on titanium surfaces with regular micro-ranged geometry, filaments are shortened, less aligned and they concentrate at the top of the geometric structures. Changes to the cytoskeleton network, i. e., its localization, alignment, orientation, and lengths of the filaments, as well as the overall concentration and distribution of key-actors are induced. For example, integrin, is distributed homogeneously, whereas vinculin, like integrin a component of focal adhesions, has been found clustered on the micro-ranged geometries. Also, the concentration of Rho, an intracellular signaling protein related to focal adhesion regulation, was significantly reduced.
Results: To explore whether regulations associated with the focal adhesion complex can be held responsible for the changed actin filament patterns, a spatial computational model has been developed using ML-Space, a rule-based model description language, which allows dynamic nesting, and its associated Brownian-motion-based simulator. The focus has been on the deactivation of cofilin in the vicinity of the focal adhesion complex. The results underline the importance of sensing mechanisms to support a clustering of actin filament nucleation on the micro-ranged geometries, and of intracellular diffusion processes, which lead to spatially heterogeneous distributions of active (dephosphorylated) cofilin, which in turn influenced the organization of the actin network. We find, for example, that the spatial heterogeneity of key molecular actors can explain the difference in filament lengths in cells on different micro-geometries partly, but to explain the full extent, further model assumptions need to be added and validated. In particular, our findings and hypothesis referring to the role, distribution, and amount of active cofilin have still to be verified in wet-lab experiments.
Conclusion: Letting cells grow on surface structures is a possibility to shed new light on the intricate mechanisms that relate membrane and actin related dynamics in the cell. Our results underline the need for declarative expressive spatial modeling approaches that allow probing different hypotheses, and the central role of the focal adhesion complex not only for nucleating actin filaments, but also for regulating possible severing agents locally.

Note: Another publication on an application of ML-Space, a short paper on a collaboration with the Department of Medical Biochemistry and Molecular Biology, appeares in the Proceedings of the CMSB 2014.

Modeling and Simulation of Linked Lives in Demography (MoSiLLDe) DFG Project granted

In this project we will develop a new domain specific modeling language, efficient execution algorithms, bring together data-driven and hypothesis driven model development and, together with our cooperation partners from the Max Planck Institute for Demography Rostock we will develop models to analyze migration patterns between Africa and Europe.

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

The paper  "Spatio-temporal model of endogenous ROS and raft-dependent Wnt/beta-catenin signaling driving cell fate commitment in human neural progenitor cells" by Fiete Haack, Heiko Lemcke, Roland Ewald, Tareck Rharass and Adelinde M. Uhrmacher  has been accepted in the  journal PLOS Computational Biology

The article "Intensional Couplings in Variable Structure Models: An Exploration Based on Multi-Level-DEVS" has been accepted for being published in the ACM TOMACS

A research paper by Alexander Steiniger and Adelinde M. Uhrmacher on intensional couplings in variable structure models and Multi-Level-DEVS has been accepted for being published in the ACM Transactions on Modeling and Computer Simulation.

The article "Automatic Runtime Adaptation for Component-based Simulation Algorithms" has been accepted for being published in the ACM TOMACS

A research paper by Tobias Helms, Roland Ewald, Stefan Rybacki and Adelinde M. Uhrmacher on automatic runtime adaptation for component-based simulation algorithms has been accepted for being published in the ACM Transactions on Modeling and Computer Simulation.