RNDr. David Šafránek, Ph.D.
VAN GOETHEM, Simon - JACQUET, Jean-Marie - BRIM, Luboš - ŠAFRÁNEK, David.
Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization. Electronic Notes in Theoretical Computer Science, Elsevier. ISSN 1571-0661, 2013, vol. 293, no. 11.3.2013, pp. 67-81.
ŠAFRÁNEK, David - ČERVENÝ, Jan - KLEMENT, Matej - BRIM, Luboš - LAZÁR, Dušan - NEDBAL, Ladislav.
E-photosynthesis.org: Web-based platform for photosynthetic processes. 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.
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.
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.
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.
ŠAFRÁNEK, David.
Parameter Identification in Biochemical Dynamical Systems: The Model Checking Approach. 2012.
STRECK, Adam - ŠAFRÁNEK, David - BRIM, Luboš.
Parsybone: Parameter Synthesizer for Boolean Networks. 2012.
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.
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.
ŠAFRÁNEK, David.
Formal Methods in Systems Biology: Petri Net Approach. 2011.
ŠAFRÁNEK, David.
Photosynthesis in silico: An Introduction to the E-photosynthesis.org Project. 2011.
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.
ŠAFRÁNEK, David.
Towards model checking in systems biology. 2011.
NEDBAL, Ladislav - ŠAFRÁNEK, David - MACHNE, Rainer.
Cyanobacteria in silico. 2010. CZE, Mikulov. 11.11.2010 - 13.11.2010, Worldwide Activity.
KLEMENT, Matej - ŠAFRÁNEK, David - ČERVENÝ, Jan - BRIM, Luboš - NEDBAL, Ladislav.
E-photosynthesis: web software for modeling and analysis of biological processes behind photosynthesis. 2010.
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.
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.
BARNAT, Jiří - DRAŽAN, Sven - FABRIKOVÁ, Jana - ŠAFRÁNEK, David - BRIM, Luboš - ČERNÁ, Ivana - LÁNÍK, Jan.
BioDiVinE. 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.
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.
BRIM, Luboš - ŠAFRÁNEK, David - VRBAS, Jakub.
BIOMS: Biological Models Specification Tool. 2009.
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.
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.
ŠAFRÁNEK, David.
On Computational Analysis of Large ODE Models. 2009.
ŘEHÁK, Zdeněk - SMRČKA, Aleš - HOLEČEK, Jan - ŠAFRÁNEK, David - ŘEHÁK, Vojtěch.
VHDL Design Verification Tools. 2009.
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.
DRAŽAN, Sven - ŠAFRÁNEK, David - BARNAT, Jiří.
GeNeSim: Genetic Network Simulator GUI. 2008.
ŠAFRÁNEK, David.
On Algorithmic Analysis of Biological Networks. 2008.
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).
BARNAT, Jiří - BRIM, Luboš - ČERNÁ, Ivana - DRAŽAN, Sven - ŠAFRÁNEK, David.
Parallel Analysis of Genetic Regulatory Networks. Grenoble : Verimag, 2007. Towards Systems Biology Workshop 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.
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.
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.
KRAMÁREKOVÁ, Miroslava - JAKUBÍK, Daniel - ŽÁDNÍK, Martin - ŠAFRÁNEK, David.
FlowMon Cache Simulation and Analysis of Inter-Packet Gaps. Vyd. CESNET, z.s.p.o. Praha : CESNET, z.s.p.o., 2006. CESNET Technical Report Series 32/2006.
KRATOCHVÍLA, Tomáš - ŘEHÁK, Vojtěch - ŠAFRÁNEK, David.
Formal Verification of a FIFO Component in Design of Network Monitoring Hardware. In 10 years of CESNET - CESNET CONFERENCE 2006. Praha : CESNET, z.s.p.o., 2006. ISBN 978-80-239-6533-9, pp. 151-160. 2006, Praha.
SMRČKA, Aleš - HLÁVKA, Petr - ŠAFRÁNEK, David - ŘEHÁK, Vojtěch - ŠIMEČEK, Pavel - VOJNAR, Tomáš.
Formal Verification of the CRC Algorithm Properties. In Proceedings of 2nd Doctoral Workshop on Mathematical and Engineering Methods in Computer Science (MEMICS 2006). Brno : FIT BUT, 2006. ISBN 80-214-3287-X, pp. 55-62. 2006, Mikulov.
ŠAFRÁNEK, David.
Visual Coordination Networks. Brno : Masaryk University, 2006. 218 pp. PhD Thesis.
ŠAFRÁNEK, David - ŘEHÁK, Vojtěch - KRATOCHVÍLA, Tomáš - ŠIMEČEK, Pavel - HLÁVKA, Petr - VOJNAR, Tomáš.
CRC64 Algorithm Analysis and Verification. Brno : CESNET, z. s. p. o., 2005. Technical Report 27/2005.
ŠAFRÁNEK, David - ŠIMŠA, Jiří.
VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. In SOFSEM 2005: Theory and Practice of Computer Science. Heidelberg : Springer, 2005. ISBN 3-540-24302-X, pp. 320-330. Liptovský Ján.
HOLEČEK, Jan - KRATOCHVÍLA, Tomáš - ŘEHÁK, Vojtěch - ŠAFRÁNEK, David - ŠIMEČEK, Pavel.
How to Formalize FPGA Hardware Design. Praha : CESNET, z.s.p.o., 2004. CESNET Technical Report No. 04/2004.
HOLEČEK, Jan - KRATOCHVÍLA, Tomáš - ŘEHÁK, Vojtěch - ŠAFRÁNEK, David - ŠIMEČEK, Pavel.
Verification Process of Hardware Design in Liberouter Project. Praha : CESNET z.s.p.o., 2004. CESNET Technical Report No. 05/2004.
HOLEČEK, Jan - KRATOCHVÍLA, Tomáš - ŘEHÁK, Vojtěch - ŠAFRÁNEK, David - ŠIMEČEK, Pavel.
Verification Results in Liberouter Project. Praha : CESNET, z.s.p.o., 2004. CESNET Technical Report No. 03/2004.
ŠAFRÁNEK, David.
Visual Coordination Diagrams. In Proceedings of the Doctoral Symposium of 7th International Conference on the Unified Modeling Language. Lisbon, Portugal : Alanen M., Cabot J., Goulao M., Saez J. and Simmonds D. (editors), 2004. pp. 53-60. 2004, Lisbon, Portugal.
ŠAFRÁNEK, David.
Visual Specification of Systems with Heterogeneous Coordination Models. In Proceeding of 3rd International Workshop on Foundations of Coordination Languages and Software Architectures. London : ENTCS, 2004. pp. 107-121. 2004, London. Vol. 180, Issue 2.
ŠAFRÁNEK, David.
Visual Specification of Concurrent Systems. In 18th IEEE International Conference on Automated Software Engineering. Montreal, Quebec, Canada : IEEE Computer Society, 2003. ISBN 0-7695-2035-9, pp. 369-372. 6.10.2003, Montreal, Quebec, Canada.
BARNAT, Jiří - BRÁZDIL, Tomáš - KRČÁL, Pavel - ŘEHÁK, Vojtěch - ŠAFRÁNEK, David.
Model checking in IPv6 Hardware Router Design. Praha : CESNET, z. s. p. o., 2002. CESNET technical report number 8/2002.
ŠAFRÁNEK, David.
SGCCS: A Graphical Language for Real-Time Coordination. In Proceedings of 1th International Workshop on Foundations of Coordination Languages and Software Architectures. Namur, Belgium : Elsevier Science, 2002. pp. 99-114. 2002, 24.8.2002, Brno, Czech Republic. Nutno dodat presna cisla stran.
ŠAFRÁNEK, David.
SGCCS: A Graphical Language for Real-Time Systems. In Proceedings SOFSEM 2002 Student Research Forum. Milovy : Mária Bieliková, 2002. pp. 47-52. Best paper award.
CRHOVÁ, Jitka - KRČÁL, Pavel - STREJČEK, Jan - ŠAFRÁNEK, David - ŠIMEČEK, Pavel.
YAHODA: verification tools database. In Proceedings of Tools Day. Brno : FI MU, 2002. pp. 99-103. 2002, 24. 8. 2002, Brno, Czech Republic.
ŠAFRÁNEK, David.
Grafická specifikace souběžných systémů. Brno : Masarykova universita, Fakulta informatiky, 2001. 68 pp. Diplomová práce.
