Elzbieta Krepska

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We describe an efficient procedure for proving stabilization of biological systems modeled as qualitative networks or genetic regulatory networks. For scalability, our procedure uses modular proof techniques, where state-space exploration is applied only locally to small pieces of the system rather than the entire system as a whole. Our procedure exploits(More)
Distributed processing of real-world graphs is challenging due to their size and the inherent irregular structure of graph computations. We present HipG, a distributed framework that facilitates programming parallel graph algorithms by composing the parallel application automatically from the user-defined pieces of sequential work on graph nodes. To make(More)
MOTIVATION Understanding the processes involved in multi-cellular pattern formation is a central problem of developmental biology, hopefully leading to many new insights, e.g. in the treatment of various diseases. Defining suitable computational techniques for development modelling, able to perform in silico simulation experiments, is an open and(More)
Distributed processing of real-world graphs is challenging due to their size and the inherent irregular structure of graph computations. We present HIPG, a distributed framework that facilitates high-level programming of parallel graph algorithms by expressing them as a hierarchy of distributed computations executed independently and managed by the user.(More)
Petri nets are a widely used formalism to qualitatively model concurrent systems such as a biological cell. We present techniques for modelling biological processes as Petri nets for further analyses and insilico experiments. Instead of extending the formalism with ,,colours” or rates, as is most often done, we focus on preserving the simplicity of the(More)
This position paper argues that the operational modelling approaches from the formal methods community can be applied fruitfully within the systems biology domain. The results can be complementary to the traditional mathematical descriptive modelling approaches used in systems biology. We discuss one example: a recent Petri net analysis of C. elegans vulval(More)
This report documents the program and the outcomes of the Seminar 11151 ‘Formal Methods in Molecular Biology’ that took place in Dagstuhl, Germany, on 10.–15. April, 2011. The most recent advances in Systems Biology were discussed, as well as and the contribution of computational formalisms to the modeling of biological systems, with the focus on(More)
In grid environments, with the large number of components (both hardware and software) that are involved in application execution, the overall probability that at least one of these components is (temporarily) non-functional is increasing rapidly. In traditional operating systems, such failures are flagged as fatal and the application will be stopped,(More)
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