RNDr. David Šafránek, Ph.D.


Kancelář: A408
Botanická 554/68a
602 00 Brno

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Telefon: 549 49 4476
E‑mail:
Životopis

Curriculum Vitae

Person Identification
  • David Šafránek, Ph.D.
    born Sep. 28, 1977 in Brno, Czechoslovakia
    nationality: Czech
Workplace
  • Work Address
    Department of Information Technologies, Faculty of Informatics, Masaryk University, Botanicka 68a, 602 00 Brno, Czech Republic

    Home Address
    Černopolní 8, 613 00 Brno, Czech Republic
Employment Position
  • Assistant Professor
Education and Academic Qualifications
  • 2006: Ph.D. in computer science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Theses: "Visual Coordination Networks". Supervisor: Doc. RNDr. Lubos Brim, CSc. Examiners: Prof. Dr. Jean-Marie Jacquet (FUNDP Namur, Belgium), Doc. RNDr. Ivana Černá, CSc. (FI MU Brno, Czech Republic).
  • 2001: Mgr. (master's degree) in computer science, Faculty of Informatics, Masaryk University, Brno, Czech Republic. Theses: "Graphical specification of concurrent systems" (in Czech)
Employment Summary
  • August 2009 - now: Assistant Professor, Department of Information Technologies, Faculty of Informatics, Masaryk University.
  • February 2007 - January 2010: full-time postdoc (FP6 NEST project EC-MOAN), Department of Computer Science, Faculty of Informatics, Masaryk University.
  • April 2005 - January 2007: Institute for Theoretical Computer Science, Faculty of Informatics, Masaryk University, junior researcher
  • January 2007 - December 2009: CESNET, z.s.p.o., Prague (Programmable Hardware research activity); junior researcher
Pedagogical Activities
  • Teaching activities
  • Fall 2008 - now: development of a new study branch and teaching the subjects Introduction to Systems Biology, Modeling and Prediction in Systems Biology, Formal Methods in Systems Biology, Computational Methods in Systems Biology, Systems Biology Seminar
  • Fall 2002 - now: Introduction to Functional Programming (exercises)
  • 2009 - 2012: Innovation of bachelor and master degree programes in the direction to systems biology (ESF)
    Student supervision 2011 - now
  • Number of supervised bachelor theses: 14
  • Number of supervised master theses: 13
  • Number of co-advised doctoral students: 3
Scientific and Research Activities
  • April 2016 - now: coordinator of Computer Science research group in The National Infrastructure for Systems Biology (C4SYS), http://c4sys.cz
  • August 2009 - now: leading member of Laboratory of Systems Biology (Sybila - http://sybila.fi.muni.cz)
  • June 2009 - now: coordinator of CyanoTeam Bioinformatics group (http://www.cyanoteam.org)
  • February 2007 - January 2010: PostDoc on FP6-STREP-NEST project no. 043235 "Escherichia coli modeling and analysis" (EC-MOAN - http://www.ec-moan.org)
  • January 2000 - December 2009: member of Parallel and Distributed Systems Laboratory (ParaDiSe - http://www.fi.muni.cz/paradise)
  • January 2002 - December 2009: coordinator of verification research group in Liberouter project (funded by CESNET, FP5-IST-2001-32603 and FP6-IST-511082; http://www.liberouter.org)
  • Research Interests: Model checking, formal verification; Bioinformatics; Modeling and computational techniques in systems biology
Academical Stays
  • November 2013: University of Oxford, UK
  • January 2009: CWI Amsterdam, The Netherlands
  • June 2008: CWI Amsterdam, The Netherlands
  • September - October 2005: Faculté d'informatique, Facultés Universitaires Notre-Dame de la Paix, Namur, Belgie
  • October 2004: Universidade Nova de Lisboa, Portugalsko
Appreciation of Science Community
  • 2009: Dagstuhl seminar on Formal Methods in Molecular Biology
  • 2007: awarded the dean's prize for a distinguished Ph.D. thesis, Faculty of Informatics, Masaryk University
  • 2002: best paper award, Ph.D. forum, SOFSEM 2002 conference
Selected Publications
  • BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. Parallel SMT-Based Parameter Synthesis with Application to Piecewise Multi-Affine Systems. In Cyrille Artho et al.. Automated Technology for Verification and Analysis. ATVA 2016. LNCS 9938. Neuveden: Springer International Publishing, 2016. s. 192-208, 17 s. ISBN 978-3-319-46519-7. doi:10.1007/978-3-319-46520-3_13. info
  • DEMKO, Martin, Nikola BENEŠ, Luboš BRIM, Samuel PASTVA a David ŠAFRÁNEK. High-Performance Symbolic Parameter Synthesis of Biological Models: A Case Study. In Ezio Bartocci et al.. Computational Methods in Systems Biology. CMSB 2016. LNBI 9859. Neuveden: Springer International Publishing, 2016. s. 82-97, 16 s. ISBN 978-3-319-45176-3. doi:10.1007/978-3-319-45177-0_6. info
  • HAJNAL, Matej, David ŠAFRÁNEK, Martin DEMKO, Samuel PASTVA, Pavel KREJČÍ a Luboš BRIM. Toward Modelling and Analysis of Transient and Sustained Behaviour of Signalling Pathways. In Eugenio Cinquemani. Hybrid Systems Biology. HSB 2016. LNBI 9957. Neuveden: Springer International Publishing, 2016. s. 57-66, 10 s. ISBN 978-3-319-47150-1. doi:10.1007/978-3-319-47151-8_4. info
  • BENEŠ, Nikola, Luboš BRIM, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. A Model Checking Approach to Discrete Bifurcation Analysis. In John S. Fitzgerald et al.. Formal Methods. FM 2016. LNCS 9995. Neuveden: Springer International Publishing, 2016. s. 85-101, 17 s. ISBN 978-3-319-48988-9. doi:10.1007/978-3-319-48989-6_6. info
  • TROJÁK, Matej, David ŠAFRÁNEK, Jakub HRABEC, Jakub ŠALAGOVIČ, Františka ROMANOVSKÁ a Jan ČERVENÝ. E-Cyanobacterium.org: A Web-Based Platform for Systems Biology of Cyanobacteria. In Ezio Bartocci et al.. Computational Methods in Systems Biology. CMSB 2016. Heidelberg: Springer, 2016. s. 316-322, 7 s. ISBN 978-3-319-45176-3. doi:10.1007/978-3-319-45177-0_20. URL info
  • DĚD, Tadeáš, David ŠAFRÁNEK, Matej TROJÁK, Matej KLEMENT, Jakub ŠALAGOVIČ a Luboš BRIM. Formal Biochemical Space with Semantics in Kappa and BNGL. In Loic Pauleve et al.. The 6th International Workshop on Static Analysis and Systems Biology, SASB 2015. ENTCS 326. Neuveden: Elsevier, 2016. s. 27-49, 23 s. ISSN 1571-0661. doi:10.1016/j.entcs.2016.09.017. info
  • BRIM, Luboš, Juraj NIŽNAN a David ŠAFRÁNEK. Compact Representation of Photosynthesis Dynamics by Rule-based Models. In 5th International Workshop on Static Analysis and Systems Biology (SASB 2014). 316. vyd. Neuveden: Elsevier, 2015. s. 17-27, 11 s. ISSN 1571-0661. doi:10.1016/j.entcs.2015.06.008. info
  • BRIM, Luboš, Milan ČEŠKA, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. Parameter Synthesis by Parallel Coloured CTL Model Checking. In Roux, Olivier and Bourdon, Jérémie. Computational Methods in Systems Biology. Neuveden: Springer International Publishing, 2015. s. 251-263, 13 s. ISBN 978-3-319-23400-7. doi:10.1007/978-3-319-23401-4_21. info
  • BRIM, Luboš, Martin DEMKO, Samuel PASTVA a David ŠAFRÁNEK. High-Performance Discrete Bifurcation Analysis for Piecewise-Affine Dynamical Systems. In Alessandro Abate, David Šafránek. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. LNCS 9271. Neuveden: Springer International Publishing, 2015. s. 58-74, 17 s. ISBN 978-3-319-26915-3. doi:10.1007/978-3-319-26916-0_4. elektronická verze v nakladatelství Springer info
  • ALESSANDRO, Abate a David ŠAFRÁNEK. Hybrid Systems Biology Fourth International Workshop, HSB 2015, Madrid, Spain, September 4-5, 2015. Revised Selected Papers. In Lecture Notes in Bioinformatics. : Springer International Publishing, 2015. 263 s. ISBN 978-3-319-26915-3. doi:10.1007/978-3-319-26916-0. elektronická verze v nakladatelství Springer info
  • BRIM, Luboš, Petr DLUHOŠ, David ŠAFRÁNEK a Tomáš VEJPUSTEK. STL*: Extending signal temporal logic with signal-value freezing operator. Information and computation, Academic Press, 2014, roč. 236, January, s. 52-67. ISSN 0890-5401. doi:10.1016/j.ic.2014.01.012. info
  • ČEŠKA, Milan, David ŠAFRÁNEK, Sven DRAŽAN a Luboš BRIM. Robustness Analysis of Stochastic Biochemical Systems. Plos One, SAN FRANCISCO: PUBLIC LIBRARY SCIENCE, 2014, roč. 9, č. 4, s. 1-23. ISSN 1932-6203. doi:10.1371/journal.pone.0094553. URL info
  • VAN GOETHEM, Simon, Jean-Marie JACQUET, Luboš BRIM a David ŠAFRÁNEK. 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. s. 67-81, 15 s. ISSN 1571-0661. doi:10.1016/j.entcs.2013.02.019. URL info
  • BRIM, Luboš, Vilém DĚD a David ŠAFRÁNEK. Qualitative modelling and analysis of Photosystem II. In CEUR Workshop Proceedings. Aachen: Neuveden, 2013. s. 17-29, 13 s. ISSN 1613-0073. URL info
  • KLEMENT, Matej, David ŠAFRÁNEK, Tadeáš DĚD, Aleš PEJZNOCH, Ladislav NEDBAL, Ralf STEUER, Jan ČERVENÝ a Stefan MUELLER. 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. s. 61-67, 7 s. ISSN 1571-0661. doi:10.1016/j.entcs.2013.11.006. URL info
  • BRIM, Luboš, Milan ČEŠKA a David ŠAFRÁNEK. Model Checking of Biological Systems. In Marco Bernardo. Formal Methods for Dynamical Systems. Neuveden: Springer, 2013. s. 63-112, 50 s. ISBN 978-3-642-38873-6. doi:10.1007/978-3-642-38874-3_3. info
  • BRIM, Luboš, Tomáš VEJPUSTEK, David ŠAFRÁNEK a Jana FABRIKOVÁ. Robustness Analysis for Value-Freezing Signal Temporal Logic. In Proceedings HSB 2013. Neuveden: Neuveden, 2013. s. 20-36, 17 s. ISSN 2075-2180. doi:10.4204/EPTCS.125. URL info
  • STRECK, Adam, Juraj KOLČÁK, Heike SIEBERT a David ŠAFRÁNEK. Esther: Introducing an Online Platform for Parameter Identification of Boolean Networks. In A. Gupta. Computational Methods in Systems Biology 11th International Conference, CMSB 2013, Klosterneuburg, Austria, September 22-24, 2013, Proceedings. Heidelberg: Springer, 2013. s. 257-258, 2 s. ISBN 978-3-642-40707-9. info
  • ŠAFRÁNEK, David. Model Checking in Systems Biology. In Formal Methods for Dynamical Systems - 13th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2013, Bertinoro. 2013. URL info
  • ŠAFRÁNEK, David. Model Checking of Biological Systems. In Oxford Talks, University of Oxford. 2013. URL info
  • BARNAT, Jiří, Luboš BRIM, Adam KREJČÍ, Adam STRECK, David ŠAFRÁNEK, Martin VEJNÁR a Tomáš VEJPUSTEK. On Parameter Synthesis by Parallel Model Checking. IEEE/ACM Transactions on Computational Biology and Bioinformatics, Los Alamitos: IEEE Computer Society, 2012, roč. 9, č. 3, s. 693-705. ISSN 1545-5963. doi:10.1109/TCBB.2011.110. URL info
  • DLUHOŠ, Petr, Luboš BRIM a David ŠAFRÁNEK. On Expressing and Monitoring Oscillatory Dynamics. Electronic Proceedings in Theoretical Computer Science, Newcastle Upon Tyne: EPTCS, 2012, roč. 2012, č. 92, s. 73-87. ISSN 2075-2180. doi:10.4204/EPTCS.92. URL info
  • KLARNER, Hannes, Adam STRECK, David ŠAFRÁNEK, Juraj KOLČÁK a Heike SIEBERT. 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. s. 207-226, 20 s. ISBN 978-3-642-33635-5. doi:10.1007/978-3-642-33636-2_13. URL info
  • BRIM, Luboš, Jana FABRIKOVÁ, Sven DRAŽAN a David ŠAFRÁNEK. On Approximative Reachability Analysis of Biochemical Dynamical Systems. In Corrado Priami et al.. Transactions on Computational Systems Biology XIV. Heidelberg: Springer, 2012. s. 77-101, 25 s. ISBN 978-3-642-35523-3. doi:10.1007/978-3-642-35524-0_4. URL info
  • ŠAFRÁNEK, David, Jan ČERVENÝ, Matej KLEMENT, Jana POSPÍŠILOVÁ, Luboš BRIM, Dušan LAZÁR a Ladislav NEDBAL. E-photosynthesis: Web-based platform for modeling of complex photosynthetic processes. BioSystems, Elsevier, 2011, roč. 103, č. 2, s. 115-124. ISSN 0303-2647. doi:10.1016/j.biosystems.2010.10.013. URL info
  • COLLINS, Pieter, Luc HABETS, Jan VAN SCHUPPEN, Ivana ČERNÁ, Jana FABRIKOVÁ a David ŠAFRÁNEK. Abstraction of Biochemical Reaction Systems on Polytopes. In Proceedings of the 18th IFAC World Congress. Milano: IFAC, 2011. s. 14869-14875, 7 s. ISBN 978-1-1234-7890-2. URL info
  • BRIM, Luboš, Jana FABRIKOVÁ, Sven DRAŽAN a David ŠAFRÁNEK. Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation. Electronic Proceedings in Theoretical Computer Science, 2011, Neuveden, č. 67, s. 97-112. ISSN 2075-2180. doi:10.4204/EPTCS.67.9. URL info
  • BARNAT, Jiří, Luboš BRIM a David ŠAFRÁNEK. High-performance analysis of biological systems dynamics with the DiVinE model checker. Briefings in Bioinformatics, Oxford (UK): Oxford University Press, 2010, roč. 11, č. 3, s. 301-312. ISSN 1467-5463. DOI Abstract PDF reprint info
  • BARNAT, Jiří, Luboš BRIM, David ŠAFRÁNEK a Martin VEJNÁR. 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. s. 95-104, 10 s. ISBN 978-0-7695-4265-2. info
  • BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN, Jana FABRIKOVÁ a David ŠAFRÁNEK. On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking. Theoretical Computer Science, 2009, roč. 2009, č. 410, s. 3128-3148. ISSN 0304-3975. URL info
  • BARNAT, Jiří, Luboš BRIM, Ivana ČERNÁ, Sven DRAŽAN, Jana FABRIKOVÁ, Jan LÁNÍK, David ŠAFRÁNEK a Ma HONGWU. BioDiVinE: A Framework for Parallel Analysis of Biological Models. In Proceedings of 2nd International Workshop on Computational Models for Cell Processes. Neuveden: EPTCS, 2009. s. 31-45, 15 s. ISSN 2075-2180. info
  • SMRČKA, Aleš, Vojtěch ŘEHÁK, Tomáš VOJNAR, David ŠAFRÁNEK, Petr MATOUŠEK a Zdeněk ŘEHÁK. 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. s. 148-164, 16 s. ISBN 978-3-540-70951-0. info
  • ŠAFRÁNEK, David. Visual Coordination Networks. Brno: Masaryk University, 2006. 218 s. PhD Thesis. info
  • ŠAFRÁNEK, David a Jiří ŠIMŠA. VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures. In SOFSEM 2005: Theory and Practice of Computer Science. Heidelberg: Springer, 2005. s. 320-330, 10 s. ISBN 3-540-24302-X. info

2016/09/18

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