RNDr. David Šafránek, Ph.D.

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found: 46 records, displayed 1 - 30

 
2014

KLEMENT, Matej - DĚD, Tadeáš - ŠAFRÁNEK, David - ČERVENÝ, Jan - MUELLER, Stefan - STEUER, Ralf.
Biochemical Space: A Framework for Systemic Annotation of Biological Models. In Proceedings of the 5th International Workshop on Interactions between Computer Science and Biology (CS2Bio’14). Amsterdam : Elsevier, 2014. 31–44-14 pp. 2014, Berlin.


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ČEŠKA, Milan - ŠAFRÁNEK, David - DRAŽAN, Sven - BRIM, Luboš.
Robustness Analysis of Stochastic Biochemical Systems. Plos One, SAN FRANCISCO, PUBLIC LIBRARY SCIENCE, USA. ISSN 1932-6203, 2014, vol. 9, no. 4, pp. 1-23.


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BRIM, Luboš - DLUHOŠ, Petr - ŠAFRÁNEK, David - VEJPUSTEK, Tomáš.
STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation, Academic Press. ISSN 0890-5401, 2014, vol. 236, no. January, pp. 52-67.


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2013

KLEMENT, Matej - ŠAFRÁNEK, David - DĚD, Tadeáš - PEJZNOCH, Aleš - NEDBAL, Ladislav - STEUER, Ralf - ČERVENÝ, Jan - MUELLER, Stefan.
A Comprehensive Web-based Platform For Domain-Specific Biological Models. In Proceedings of the fourth International Workshop on Interactions between Computer Science and Biology (CS2Bio'13). Neuveden : Elsevier, 2013. pp. 61-67. 2013, Florencie.


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STRECK, Adam - KOLČÁK, Juraj - SIEBERT, Heike - ŠAFRÁNEK, David.
Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks. In Computational Methods in Systems Biology 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings. Heidelberg : Springer, 2013. ISBN 978-3-642-40707-9, pp. 257-258. 2013, Vienna.


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BRIM, Luboš - ČEŠKA, Milan - DRAŽAN, Sven - ŠAFRÁNEK, David.
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking. In 25th International Conference, CAV 2013, Saint Petersburg, Russia, July 13-19, 2013. Proceedings. Berlin : Springer Berlin Heidelberg, 2013. ISBN 978-3-642-39798-1, pp. 107-123. 2013, Saint Petersburg.


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BRIM, Luboš - ČEŠKA, Milan - ŠAFRÁNEK, David.
Model Checking of Biological Systems. In Formal Methods for Dynamical Systems. Neuveden : Springer, 2013. ISBN 978-3-642-38873-6, pp. 63-112. 2013, Bertinoro.


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BRIM, Luboš - DĚD, Vilém - ŠAFRÁNEK, David.
Qualitative modelling and analysis of Photosystem II. In CEUR Workshop Proceedings. Aachen : Neuveden, 2013. pp. 17-29. 2013, Milano.


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BRIM, Luboš - VEJPUSTEK, Tomáš - ŠAFRÁNEK, David - FABRIKOVÁ, Jana.
Robustness Analysis for Value-Freezing Signal Temporal Logic. In Proceedings HSB 2013. Neuveden : Neuveden, 2013. pp. 20-36. 2013, Taormina.


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BRIM, Luboš - ČEŠKA, Milan - DRAŽAN, Sven - ŠAFRÁNEK, David.
Robustness Analysis of Stochastic Systems. In Electronic Proceedings in Theoretical Computer Science, Volume 116. Turku : Open Publishing Association, 2013. pp. 33-34.


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VAN GOETHEM, Simon - JACQUET, Jean-Marie - BRIM, Luboš - ŠAFRÁNEK, David.
Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. In Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12). Neuveden : Elsevier, 2013. pp. 67-81. 2012, Florencie.


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2012

BRIM, Luboš - FABRIKOVÁ, Jana - DRAŽAN, Sven - ŠAFRÁNEK, David.
On Approximative Reachability Analysis of Biochemical Dynamical Systems. In Transactions on Computational Systems Biology XIV. Heidelberg : Springer, 2012. ISBN 978-3-642-35523-3, pp. 77-101. 2012, Aachen.


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DLUHOŠ, Petr - BRIM, Luboš - ŠAFRÁNEK, David.
On Expressing and Monitoring Oscillatory Dynamics. Electronic Proceedings in Theoretical Computer Science, Newcastle Upon Tyne, EPTCS. ISSN 2075-2180, 2012, vol. 2012, no. 92, pp. 73-87.


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BARNAT, Jiří - BRIM, Luboš - KREJČÍ, Adam - STRECK, Adam - ŠAFRÁNEK, David - VEJNÁR, Martin - VEJPUSTEK, Tomáš.
On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Los Alamitos, IEEE Computer Society. ISSN 1545-5963, 2012, vol. 9, no. 3, pp. 693-705.


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KLARNER, Hannes - STRECK, Adam - ŠAFRÁNEK, David - KOLČÁK, Juraj - SIEBERT, Heike.
Parameter Identification and Model Ranking of Thomas Networks. In Computational Methods in Systems Biology: 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings. Berlin : Springer, 2012. ISBN 978-3-642-33635-5, pp. 207-226. 2012, London.


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2011

COLLINS, Pieter - HABETS, Luc - VAN SCHUPPEN, Jan - ČERNÁ, Ivana - FABRIKOVÁ, Jana - ŠAFRÁNEK, David.
Abstraction of Biochemical Reaction Systems on Polytopes. In Proceedings of the 18th IFAC World Congress. Milano : IFAC, 2011. ISBN 978-1-1234-7890-2, pp. 14869-14875. 2011, Milano.


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ŠAFRÁNEK, David - ČERVENÝ, Jan - KLEMENT, Matej - POSPÍŠILOVÁ, Jana - BRIM, Luboš - LAZÁR, Dušan - NEDBAL, Ladislav.
E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. BioSystems, Elsevier. ISSN 0303-2647, 2011, vol. 103, no. 2, pp. 115-124.


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BRIM, Luboš - FABRIKOVÁ, Jana - DRAŽAN, Sven - ŠAFRÁNEK, David.
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. Electronic Proceedings in Theoretical Computer Science, USA. ISSN 2075-2180, 2011, vol. Neuveden, no. 67, pp. 97-112.


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2010

KLEMENT, Matej - ŠAFRÁNEK, David - ČERVENÝ, Jan - BRIM, Luboš - NEDBAL, Ladislav.
E-photosynthesis: web software for modeling and analysis of biological processes behind photosynthesis. 2010.


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BARNAT, Jiří - BRIM, Luboš - ŠAFRÁNEK, David.
High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings in Bioinformatics, Oxford (UK), Oxford University Press. ISSN 1467-5463, 2010, vol. 11, no. 3, pp. 301-312.


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BARNAT, Jiří - BRIM, Luboš - ŠAFRÁNEK, David - VEJNÁR, Martin.
Parameter Scanning by Parallel Model Checking with Applications in Systems Biology. In Ninth International Workshop on Parallel and Distributed Methods in Verification, and Second International Workshop on High Performance Computational Systems Biology. Los Alamitos : IEEE Computer Society, 2010. ISBN 978-0-7695-4265-2, pp. 95-104. 2010, Enschede.


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2009

BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - FABRIKOVÁ, Jana - LÁNÍK, Jan - ŠAFRÁNEK, David - HONGWU, Ma.
BioDiVinE: A Framework for Parallel Analysis of Biological Models. In Proceedings of 2nd International Workshop on Computational Models for Cell Processes. Neuveden : EPTCS, 2009. pp. 31-45. 2009, Eindhoven.


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BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - FABRIKOVÁ, Jana - LÁNÍK, Jan - ŠAFRÁNEK, David.
BioDiVinE: A Tool for Parallel Analysis of Multi-Affine ODE Models. In Computational Mehotds in Systems Biology: Abstract of the Posters. Pisa : University of Pisa, 2009. pp. 1-5. 2009, Bologna.


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BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - FABRIKOVÁ, Jana - ŠAFRÁNEK, David.
Computational Analysis of Large-Scale Multi-Affine ODE Models. In International Workshop on High Performance Computational Systems Biology. Los Alamitos (California) : IEEE Computer Society, 2009. ISBN 978-0-7695-3809-9, pp. 81-90. 2009, Trento.


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BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - FABRIKOVÁ, Jana - ŠAFRÁNEK, David.
On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. Theoretical Computer Science. ISSN 0304-3975, 2009, vol. 2009, no. 410, pp. 3128-3148.


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2008

BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - ŠAFRÁNEK, David.
From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks. In Proceedings of PDMC 2008 - Parallel and Distributed Methods ins VerifiCation. Budapest : Ivana Cerna and Gerald Luettgen, 2008. pp. 83-96. 2008, Budapest.


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BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - ŠAFRÁNEK, David.
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE. In Electronic Notes in Theoretical Computer Science. Vyd. Vol. 194/3. Elsevier : Elsevier Science, 2008. pp. 35-50. 2007, Lisbon. Proceedings of From Biology to Concurrency and Back (FBTC 2007).


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2007

ŠAFRÁNEK, David - KOBIERSKÝ, Petr - PUŠ, Viktor - MÁLEK, Tom.
SystemVerilog verification of VHDL design. Vyd. CESNET, z.s.p.o. Praha : CESNET, z.s.p.o., 2007. CESNET Technical Reports.


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SMRČKA, Aleš - ŘEHÁK, Vojtěch - VOJNAR, Tomáš - ŠAFRÁNEK, David - MATOUŠEK, Petr - ŘEHÁK, Zdeněk.
Verifying VHDL Designs with Multiple Clocks in SMV. In Formal Methods Applications and Technology, 11th International Workshop on Formal Methods for Industrial Critical Systems, FMICS 2006, and 5th International Workshop on Parallel and Distributed Methods in Verification, PDMC 2006. Bonn : Springer-Verlag, 2007. ISBN 978-3-540-70951-0, pp. 148-164.


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2006

ŠAFRÁNEK, David.
Architectural Interoperability Checking in Visual Coordination Networks. In Combined Proceedings of the Second International Workshop on Coordination and Organization (CoOrg 2006) and the Second International Workshop on Methods and Tools for Coordinating Concurrent, Distributed and Mobile Systems (MTCoord 2006). Bologna : Elsevier Science, 2006. pp. 81-96. 2006, Bologna. vol. 181.


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