Stefan Leye

Limbus Medical Technologies GmbH

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 it...

With the rising number and diversity of simulation experiment methods, the need for a tool supporting an easy exploitation of those methods emerges. We introduce GUISE, an experiment tool to support users in conducting experiments. We structure simulation experiments according to six tasks: specification, configuration of model parameters, simulati...

Human neural progenitor cells (hNPCs) form a new prospect for replacement therapies in the context of neurodegenerative diseases. The Wnt/-catenin signaling pathway is known to be involved in the differentiation process of hNPCs. RVM cells form a common cell model of hNPCs for in vitro investigation. Previous observations in RVM cells raise the que...

We provide the details of the model in Sbml format. The parameter values correspond to the ones found in Table 3 , Set 2. (XML)

We provide details regarding the parameter sensitivity analysis. (PDF)

The integration of workflows into modeling and simulation tools promises to provide easier reproduction and provenance of simulation data and its generating process. We present the use of workflow templates and frames realized in WORMS to support and document activities involved in executing simulation experiments. Thereby we make use of functional...

While model checking is a powerful technique to analyze the properties of a model, it can be very expensive or even impossible, if the model comprises many states that have to be explored. Simulation-based model checking is an alternative, where the properties defined in temporal logics are not checked on the model itself but on traces produced dur...

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...

Dry-lab experimentation is being 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 π-Calculus is a modeling formalism for concurrent processes. Realized as part of the plug-in based modeling and simulation framework JAMES II, we propose an architecture for π-Calculus-based modeling and simulation, which supports both flexibility and efficiency. Facilitating the design of new π-Calculus-based formalisms and simulators is of pa...

Up to now, it is not possible to obtain analytical solutions for complex molecular association processes (e.g. Molecule recognition in Signaling or catalysis). Instead Brownian Dynamics (BD) simulations are commonly used to estimate the rate of diffusional association, e.g. to be later used in mesoscopic simulations. Meanwhile a portfolio of diffus...

With the rising number and diversity of validation methods, the need for a tool supporting an easy exploitation of those methods emerges. We introduce FAMVal, a validation architecture that supports the seamless integration of different validation techniques. We structure a validation experiment into the tasks specification of requirements, configu...

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, g...

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 selecti...

Model validation is essential in modeling and simulation. It "finalizes" the modeling process, and provides the base for reliable experiments with the model, and thus to gain trustworthy insights of the system under study. Diverse techniques have been developed addressing different needs and are used during different phases in the modeling and simu...

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 jobs over a set of computing resources that host simulation servic...

Compartments play an important role in molecular and cell biology modeling, which motivated the development of BETA-BINDERS, a formalism which is an extension of the pi-CALCULUS. To execute BETA-BINDERS models, sophisticated simulators are required to ensure a sound and efficient execution. Parallel and distributed simulation represents one means t...

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-dist...

Beta-binders is a comparatively new modeling formalism introduced for systems biology. To execute Beta-binders models, suitable simulators are required which translate the operational semantics of Beta-binders into a sound and efficent execution. Efficiency can be reached by parallel and distributed simulation and by a proper representation of mode...

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 interprocessor communication, since this is a major bottleneck...