David Šafránek

2013

Luboš Brim, Milan Češka, Sven Dražan, and David Šafránek:
Exploring Parameter Space of Stochastic Biochemical Systems Using Quantitative Model Checking,
Computer Aided Verification: 25th International Conference, CAV 2013, Saint Petersburg, Russia, July 13-19, 2013. Proceedings, Springer Berlin Heidelberg, 2013, 107–123. [bibtex, url]

Luboš Brim, Milan Češka, and David Šafránek:
Model Checking of Biological Systems,
Formal Methods for Dynamical Systems: 13th International School on Formal Methods for the Design of Computer, Communication, and Software Systems, SFM 2013, Bertinoro, Italy, June 17-22, 2013. Advanced Lectures, Springer Berlin Heidelberg, 2013, 63–112. [bibtex, url]

Luboš Brim, Milan Češka, Sven Dražan, and David Šafránek:
On Robustness Analysis of Stochastic Biochemical Systems by Probabilistic Model Checking,
arXiv preprint arXiv:1310.4734, 2013. [bibtex]

Luboš Brim, Vilém Děd, and David Šafránek:
Qualitative modelling and analysis of Photosystem II,
CEUR Workshop Proceedings, Neuveden, 2013, 17-29. [bibtex, url]

Luboš Brim, Tomáš Vejpustek, David Šafránek, and Jana Fabriková:
Robustness Analysis for Value-Freezing Signal Temporal Logic,
Proceedings HSB 2013, Neuveden, 2013, 20-36. [bibtex, url]

S. Van Goethem, J. M. Jacquet, Luboš Brim, and David Šafránek:
Timed Modelling of Gene Networks with Arbitrarily Precise Expression Discretization,
Electron. Notes Theor. Comput. Sci., Elsevier Science Publishers B. V., 2013, 67–81. [bibtex, url]

2012

Jiří Barnat, Luboš Brim, Adam Krejci, Adam Streck, David Šafránek, Martin Vejnár, and Tomáš Vejpustek:
On Parameter Synthesis by Parallel Model Checking,
IEEE/ACM Trans. Comput. Biol. Bioinformatics, IEEE Computer Society Press, 2012, 693–705. [bibtex, url]

2011

Pieter Collins, Luc Habets, Jan van Schuppen, Ivana Černá, Jana Fabriková, and David Šafránek:
Abstraction of Biochemical Reaction Systems on Polytopes,
Proceedings of the 18th IFAC World Congress, IFAC, 2011, 14869-14875. [bibtex, url]

Luboš Brim, Jana Fabriková, Sven Dražan, and David Šafránek:
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation,
Electronic Proceedings in Theoretical Computer Science, 2011. [bibtex, url]

2010

Jiří Barnat, Luboš Brim, and David Šafránek:
High-Performance Analysis of Biological Systems Dynamics with the DiVinE Model Checker,
Briefings in Bioinformatics, 2010, 301–312. [bibtex, url]

Jiří Barnat, Luboš Brim, David Šafránek, and Martin Vejnár:
Parameter Scanning by Parallel Model Checking with Applications in Systems Biology,
Proceedings of joint HiBi/PDMC workshop (HiBi/PDMC 2010), IEEE, 2010. [bibtex]

2009

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, Jan Láník, David Šafránek, and Hongwu Ma:
BioDiVinE: A Framework for Parallel Analysis of Biological Models,
Electronic Proceedings in Theoretical Computer Science (COMPMOD 2009), 2009, 31–45. [bibtex, url]

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, Jan Láník, and David Šafránek:
BioDiVinE: A Tool for Parallel Analysis of Multi-Affine ODE Models,
Proceedings of The 7th Conference on Computational Methods in Systems Biology (CMSB’09), Universita di Pisa, 2009, volume TR-09-09 of Technical Report, 1–5. [bibtex]

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, and David Šafránek:
Computational Analysis of Large-Scale Multi-Affine ODE Models,
2009 International Workshop on High Performance Computational Systems Biology (HiBi 2009), IEEE Computer Society Press, 2009, 81–90. [bibtex]

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, and David Šafránek:
On algorithmic analysis of transcriptional regulation by LTL model checking,
Theor. Comput. Sci., 2009, 3128–3148. [bibtex, url]

2008

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, and David Šafránek:
From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks,
Proceedings of PDMC 2008 - Parallel and Distributed Methods ins VerifiCation, Ivana Černá and Gerald Luettgen, 2008, 83-96. [bibtex]

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, and David Šafránek:
Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE,
ENTCS, Elsevier, 2008, volume 194 of ENTCS, 35–50. [bibtex]

2007

Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, and David Šafránek:
Parallel Model-Checking Genetic Regulatory Networks,
Towards Systems Biology, Verimag, 2007. [bibtex]

2004

David Šafránek:
Visual Coordination Diagrams,
Proceedings of the Doctoral Symposium of 7th International Conference on the Unified Modeling Language, Alanen M., Cabot J., Goulao M., Saez J. and Simmonds D. (editors), 2004, 53-60. [bibtex, url]

David Šafránek:
Visual Specification of Systems with Heterogeneous Coordination Models,
Proceeding of 3rd International Workshop on Foundations of Coordination Languages and Software Architectures, ENTCS, 2004, 107-121. [bibtex]

2003

David Šafránek:
Visual specification of concurrent systems,
Automated Software Engineering, 2003. Proceedings. 18th IEEE International Conference on, 2003, 369-372. [bibtex, url]

2002

Jiří Barnat, Tomáš Brázdil, Pavel Krčál, Vojtěch Řehák, and David Šafránek:
Model Checking in IPv6 Hardware Router Design,
2002, 8. [bibtex]

David Šafránek:
SGCCS: A Graphical Language for Real-Time Coordination,
Proceedings of 1th International Workshop on Foundations of Coordination Languages and Software Architectures, Elsevier Science, 2002, 99-114. [bibtex, url]

David Šafránek:
SGCCS: A Graphical Language for Real-Time Systems,
Proceedings SOFSEM 2002 Student Research Forum, Mária Bieliková, 2002, 47-52. [bibtex, url]

Jitka Crhová, Pavel Krčál, Jan Strejček, David Šafránek, and Pavel Šimeček:
YAHODA: verification tools database,
Proceedings of Tools Day, FI MU, 2002, 99-103. [bibtex, url]