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Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation [article]

Lubos Brim and Jana Fabrikova and Sven Drazan and David Safranek
2011 arXiv   pre-print
In this paper a novel computational technique for finite discrete approximation of continuous dynamical systems suitable for a significant class of biochemical dynamical systems is introduced. The method is parameterized in order to affect the imposed level of approximation provided that with increasing parameter value the approximation converges to the original continuous system. By employing this approximation technique, we present algorithms solving the reachability problem for biochemical
more » ... namical systems. The presented method and algorithms are evaluated on several exemplary biological models and on a real case study. This is a full version of the paper published in the proceedings of CompMod 2011.
arXiv:1107.5924v1 fatcat:hrxrx4w36zhfboilt35jkn4zfa

Abstraction of Biochemical Reaction Systems on Polytopes

Pieter J. Collins, Luc Habets, Jan H. van Schuppen, Ivana Černá, Jana Fabriková, David Šafránek
2011 IFAC Proceedings Volumes  
Analysis of the dynamic behavior of large-scale biochemical reaction systems can be facilitated by abstraction followed by model checking. A biochemical reaction system can be approximated by a multi-affine system or an affine system on a rectangle. Either of these systems can be abstracted to an automaton. Model checking can then be employed to determine whether the dynamic behavior of the automaton satisfies specific properties. A relation between the system and its abstraction is proved; it
more » ... s an over-approximation: any discrete state trajectory of the abstraction of the continuous state trajectory is contained in the automaton, but the automaton may contain more behavior.
doi:10.3182/20110828-6-it-1002.03317 fatcat:2nwpswtehrdkphxkilxiroupcq

Computational Analysis of Large-Scale Multi-affine ODE Models

Lubos Brim, Jiri Barnat, Ivana Cerna, Sven Drazan, Jana Fabrikova, David Safranek
2009 2009 International Workshop on High Performance Computational Systems Biology  
A biological system as considered in systems biology is understood in the form of a network of interactions among individual biochemical species. Complexity of these networks is inherently enormous, even for simple (e.g., procaryotic) organisms. When modeling and analyzing dynamics of these networks, i.e., exploring how the species evolve in time, we have to fight even another level of complexity -the enormous state space. In this paper we deal with a class of biological models that can be
more » ... ibed in terms of multi-affine dynamic systems. First, we present a prototype tool for parallel (distributed) analysis of multi-affine systems discretized into rectangles that adapts the approach of Belta [1], [2] . Secondly, we propose heuristics that significantly increase applicability of the approach to large biological models. Effects of different settings of the heuristics is firstly compared on a set of experiments performed on small models. Subsequently, experiments on large models are provided as well.
doi:10.1109/hibi.2009.14 fatcat:opqtc34plzbzfnkgmlctk7ywva

BioDiVinE: A Framework for Parallel Analysis of Biological Models

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, Jan Láník, David Šafránek, Hongwu Ma
2009 Electronic Proceedings in Theoretical Computer Science  
In this paper a novel tool BioDiVinEfor parallel analysis of biological models is presented. The tool allows analysis of biological models specified in terms of a set of chemical reactions. Chemical reactions are transformed into a system of multi-affine differential equations. BioDiVinE employs techniques for finite discrete abstraction of the continuous state space. At that level, parallel analysis algorithms based on model checking are provided. In the paper, the key tool features are
more » ... ed and their application is demonstrated by means of a case study.
doi:10.4204/eptcs.6.3 fatcat:dxboa3v4anbybi4ehzaa4opcci

Community Life of Slovaks in Budapest between 1850 and 1875

2016 Social Pathology and Prevention  
Politické aktivity Jána Nepomuka Bobulu, Prešov 2014; DEMMEL, József: Magyar haza, szlovák nemzet.  ...  Headed by Ján Nepomuk Bobula, the New School was headquartered in the Fabriková street in Theresa Town, organized around the magazine Slovenské noviny (1868-1875) and its members and sympathizers met under  ... 
doi:10.25142/cep.2016.015 fatcat:u6alkscppnbvtl6vamlwmvtlgm

Formal Methods in Molecular Biology Dagstuhl Seminar

Rainer Breitling, David Gilbert, Monika Heiner, Corrado Priami
, Jana Detecting Inconsistencies in Large Biological Networks with Answer Set Programming Torsten Schaub (Universität Potsdam, DE) Keywords: Answer Set Programming, consistency, data set evaluation Joint  ...  Cell Cycle coupling Alessandro Romanel (Microsoft Research -University Trento, IT) model checking checking Joint work of: afránek, David; Barnat, Ji°í; Brim, Lubo²; erná, Ivana; Draºan, Sven; Fabriková  ...