Publications

• related to computational methods in systems biology

  Timed Modelling of Gene Networks with Arbitrary Expression Level Discretization
  with S. Van Goethem, J-M. Jacquet, and L. Brim
  Proceedings of the Third International Workshop on Interactions Between Computer Science and Biology (CS2Bio'12), Electronic Notes in Computer Science, Volume 293, 11 March 2013, Pages 67-81. Elsevier.

  Abstract      DOI (c) Elsevier

  Parameter Identification and Model Ranking of Thomas Networks
  with H. Klarner, A. Streck, J. Kolcak, and H. Siebert
  Computational Methods in Systems Biology 10th International Conference, CMSB 2012, London, UK, October 3-5, 2012. Proceedings., Lecture Notes in Computer Science, vol. 7605, 2012, pp 207-226. Springer.

  Abstract      DOI (c) Springer    Full version PDF (c) 2012 FI MU

  On Approximative Reachability Analysis of Biochemical Dynamical Systems
  with L. Brim, J. Fabrikova, and S. Drazan
  Transactions on Computational Systems Biology XIV, Lecture Notes in Computer Science, vol. 7625, 2012, pp 77-101. Springer.

  Abstract      DOI (c) Springer

  On Expressing and Monitoring Oscillatory Dynamics
  with P. Dluhos and L. Brim
  Proceedings of First International Workshop on Hybrid Systems Biology 2012, EPTCS 92, 2012, pp 73-87.

  Abstract      DOI (c) Springer

  On Parameter Synthesis by Parallel Model Checking
  with J. Barnat, L. Brim, A. Krejci, A. Streck, M. Vejnar, and T. Vejpustek
  IEEE/ACM Transactions on Computational Biology and Bioinformatics. May-June 2012;9(3):693-705

  Abstract      DOI (c) IEEE Computer Society

  Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation
  with L. Brim, J. Fabrikova, and S. Drazan
  In Proceedings of 3rd International Workshop on Computational Models for Cell Processes (COMPMOD 2011). EPTCS 67, 2011, pp. 97-112.

  Abstract      PDF (preprint)      DOI      Full version PDF (arXiv.org)

  Abstraction of Biochemical Reaction Systems on Polytopes
  with P. Collins, L. Habets, J.H. van Schuppen, I. Cerna, and J. Fabrikova
  In Proceedings of 18th IFAC World Congress In press. (2011)

  Abstract      PDF (preprint)

  Parameter Scanning by Parallel Model Checking with Applications in Systems Biology
  with J. Barnat, L. Brim, and M. Vejnar
  in Proceedings of HIBI 2010, pp. 95-104, IEEE Computer Society, 2010.

  Abstract      PDF (preprint)

  High-performance analysis of biological systems dynamics with the DiVinE model checker
  with J. Barnat and L. Brim
  Briefings in Bioinformatics 11(3):301-12 (2010)

  Abstract      PDF (Oxford University Press)     DOI

  BioDiVinE: A Framework for Parallel Analysis of Biological Models
  with J. Barnat, L. Brim, I. Cerna, S. Drazan, J. Fabrikova, J. Lanik, and H. Ma
  in Proceedings of 2nd International Workshop on Computational Models for Cell Processes (COMPMOD 2009), pp. 31-45, EPTCS 6, 2009.

  Abstract      PDF (preprint)     DOI (final version online)

  BioDiVinE: A Tool for Parallel Analysis of Multi-Affine ODE Models
  with J. Barnat, L. Brim, I. Cerna, S. Drazan, J. Fabrikova, and J. Lanik
  in Computational Methods in Systems Biology: Abstracts of the Posters, University of Pisa, Technical Report TR-09-09, p. 1-4, 2009.

  Extended Abstract      Poster

  Computational Analysis of Large-Scale Multi-Affine ODE Models
  with J. Barnat, L. Brim, I. Cerna, S. Drazan, and J. Fabrikova
  in Proceedings of High Performance Computational Systems Biology (HiBi 2009), pp. 81-90, IEEE Computer Society, 2009.

  Abstract      PDF (preprint)

  On Algorithmic Analysis of Transcriptional Regulation by LTL Model Checking
  with J. Barnat, L. Brim, I. Cerna, S. Drazan, and J. Fabrikova
  in Theoretical Computer Science 410, pp. 3128-3148, 2009.

  Abstract      DOI (final version online)

  From Simple Regulatory Motifs to Parallel Model Checking of Complex Transcriptional Networks
  with J. Barnat, L. Brim, I. Cerna, and S. Drazan
  in Proceedings of Parallel and Distributed Methods in Verification (PDMC 2008), p. 83-96, 2008.

  Abstract      Postscript (preprint)

  Parallel Model Checking Large-Scale Genetic Regulatory Networks with DiVinE
  with J. Barnat, L. Brim, I. Cerna, and S. Drazan
  in From Biology To Concurrency and Back (FBTC 2007), ENTCS, Vol. 194/3, p. 35-50, 2008

  Abstract      Postscript (preprint)
  
  

• related to formal visual specification and coordination languages theory

  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), ENTCS, Vol. 181, p. 81-96, 2006

  Abstract      Postscript (preprint)

  VCD: A Visual Formalism for Specification of Heterogeneous Software Architectures
  with J. Simsa
  in proceedings of SOFSEM 2005: Theory and Practice of Computer Science: 31st Conference on Current Trends in Theory and Practice of Computer Science, LNCS, Vol. 3381, 01/2005

  Abstract      Postscript (Copyright (C) 2005 Springer-Verlag)      Full version (Copyright (C) 2005 FI MU)

  Visual Coordination Diagrams
  in proceedings of Doctoral Symposium of UML 2004, Lisbon, 10/2004

  Abstract      Postscript

  Visual Specification of Systems with Heterogeneous Coordination Models
  in proceedings of 3st International Workshop on Foundations of Coordination Languages and Software Architectures, ENTCS, Vol. 180/2, p. 107-121, 2004

  Abstract      Postscript (Copyright (C) 2004 Elsevier Science)

  Visual Specification of Concurrent Systems
  in proceedings of 18th IEEE International Conference on Automated Software Engineering, IEEE Computer Society, Montreal, 6/10/2003

  Abstract      Postscript (Copyright (C) IEEE Computer Society)

  SGCCS: A Graphical Language for Real-Time Systems
  

  in proceedings of Student Research Forum affiliated to SOFSEM 2002 conference, Milovy, 27/11/2002
  

  Abstract     Postscript    

  SGCCS: A Graphical Language for Real-Time Coordination
  

  in proceedings of 1st International Workshop on Foundations of Coordination Languages and Software Architectures, ENTCS, Vol. 68/3, 08/2002
  

  Abstract     Postscript (Copyright (C) 2002 Elsevier Science)    

• related to practical formal verification

  SystemVerilog verification of VHDL design
  

  with Petr Kobiersky, Tom Malek, and Viktor Pus
  CESNET Technical Report, 35/2007
  

  Abstract     PDF (Copyright (C) 2007 CESNET, z.s.p.o.)    

  Verifying VHDL Designs with Multiple Clocks in SMV
  with A. Smrcka, V. Rehak, T. Vojnar, P. Matousek and Z. Rehak
  in Formal Methods: Applications and Technology, LNCS, volume 4346, 2007

  Abstract      Postscript (Copyright (C) 2007 Springer-Verlag)

  Formal Verification of the CRC Algorithm Properties
  with P. Hlavka, V. Rehak, A. Smrcka, P. Simecek, and T. Vojnar
  in proceedings of 2nd Doctoral Workshop on Mathematical and Engineering Methods in Computer Science, 2006

  Formal Verification of a FIFO Component in Design of Network Monitoring Hardware
  

  with Tom?Kratochv?a and Vojt?h ?h?
  in proceedings of CESNET 2006 conference, CESNET z.s.p.o., 03/2006
  

  Abstract     PDF (preprint)    

  CRC64 Algorithm Analysis and Verification
  

  with Petr Hl?ka, Tom?Kratochv?a, Vojt?h ?h?, Pavel ?ime?k, and Tom?Vojnar
  CESNET Technical Report, 27/2005
  

  Abstract     Postscript (Copyright (C) 2005 CESNET, z.s.p.o.)    

  Verification Process of Hardware Design in Liberouter Project
  

  with Jan Hole?k, Tom?Kratochv?a, Vojt?h ?h? and Pavel ?ime?k
  CESNET Technical Report, 05/2004
  

  Abstract     Postscript (Copyright (C) 2004 CESNET z.s.p.o.)    

  How to Formalize FPGA Hardware Design
  

  with Jan Hole?k, Tom?Kratochv?a, Vojt?h ?h? and Pavel ?ime?k
  CESNET Technical Report, 04/2004
  

  Abstract     Postscript (Copyright (C) 2004 CESNET z.s.p.o.)    

  Verification Results in Liberouter Project
  

  with Jan Hole?k, Tom?Kratochv?a, Vojt?h ?h? and Pavel ?ime?k
  CESNET Technical Report, 03/2004
  

  Abstract     Postscript (Copyright (C) 2004 CESNET z.s.p.o.)    

  Model Checking in Design of IPv6 Hardware Router
  

  with Ji? Barnat, Tom?Br?dil, Pavel Kr?l, Vojt?h ?h?
  CESNET Technical Report, 08/2002
  

  Abstract     Postscript (Copyright (C) 2002 CESNET z.s.p.o.)    

• related to simulation

  FlowMon Cache Simulation and Analysis of Inter-Packet Gaps
  

  with M. Kramarekova, D. Jakubik, and M. Zadnik
  CESNET Technical Report, 32/2006
  

  Abstract     PDF (Copyright (C) 2006 CESNET z.s.p.o.)    

• related to tools

  E-photosynthesis: web-based platform for modeling of complex photosynthetic processes
  with J. Cerveny, M. Klement, J. Pospisilova, L. Brim, D. Lazar, and L. Nedbal
  Biosystems. 2011 Feb;103(2):115-24.

  Abstract      DOI (c) Elsevier   Poster PDF (CMSB 2012)

  YAHODA: Verification Tools Database
  

  with J.Crhov? P.Kr?l, J.Strej?k, P.?ime?k
  in proceedings of Tools Day affiliated to CONCUR 2002, FI MU Report Series, FIMU-RS-2002-05
  

  Abstract     Postscript (Copyright (C) 2002 FI MU)    

  
  

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