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Dagstuhl Seminar 11151

Formal Methods in Molecular Biology

( Apr 10 – Apr 15, 2011 )

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The second Dagstuhl Seminar on Formal Methods in Molecular Biology took place from 10--15 April, 2011. 35 participants from 8 countries gathered to discuss the most recent advances in Systems Biology and the contribution of computational formalisms to the successful modeling of biological systems. Major recurrent themes were the description of stochastic phenomena in biology, the modeling of spatial aspects of cellular behavior, and the robustness of cellular switches in the face of molecular noise and uncertainty of parameter inference. The computational modeling approaches applied to these challenges were particularly diverse, ranging from differential equation-based models to various flavors of rule-based languages, Petri Nets and process algebras.

A central component of the seminar was the Second International Biomodeling Competition. Teams formed during the first day and worked on biological case studies using a variety of modeling formalisms and analysis methods; the results were presented on Thursday afternoon and the winner determined by a joint vote of the audience.

The 1st prize went to the team of Kirill Batmanov, Antje Beyer, Matthias Jeschke and Carsten Maus, for their work on `Synchronization of cell populations'.

The 2nd prize went to the team of Andrea Bracciali, Mostafa Herajy, Pietro Lió, Chris Myers, Brett Olivier, and Natal van Riel for their work on `A bistable gene switch'.

Special prizes were awarded to the team of Chiara Bodei, Luca Bortolussi, Davide Chiarugi, Maria Luisa Guerriero, Jane Hillston Ivan Mura, Alberto Policriti, and Alessandro Romanel (for `Critical Analysis'), the team of Mary Ann Blätke, Qian Gao, David Gilbert, Simon Hardy, Monika Heiner, Andrzej Kierzek, Fei Liu and Wolfgang Marwan (for `Innovative use of Petri Nets', and the team of Maciej Dobrzynski, Mathias John, Céline Kuttler, Bartek Wilczynski and Verena Wolf (for `A pure stochastical approach').

  • Kirill Batmanov (Lille I University, FR)
  • Giampaolo Bella (University of Catania, IT)
  • Antje Beyer (University of Cambridge, GB)
  • Mary Ann Blätke (Universität Magdeburg - IBIO, DE) [dblp]
  • Chiara Bodei (University of Pisa, IT)
  • Luca Bortolussi (University of Trieste, IT) [dblp]
  • Andrea Bracciali (University of Stirling, GB)
  • Rainer Breitling (University of Manchester, GB) [dblp]
  • Davide Chiarugi (University of Siena, IT)
  • Maciej Dobrzynski (University College - Dublin, IE) [dblp]
  • Anna Gambin (University of Warsaw, PL) [dblp]
  • David Gilbert (Brunel University, GB) [dblp]
  • Maria Luisa Guerriero (University of Edinburgh, GB)
  • Simon Hardy (Mount Sinai Medical School - New York, US) [dblp]
  • Monika Heiner (BTU Cottbus, DE) [dblp]
  • Mostafa Herajy (BTU Cottbus, DE) [dblp]
  • Jane Hillston (University of Edinburgh, GB) [dblp]
  • Matthias Jeschke (Mainz, DE)
  • Mathias John (IRI - Villeneuve d'Ascq, FR)
  • Andrzej M. Kierzek (University of Surrey, GB) [dblp]
  • Elzbieta Krepska (Free University of Amsterdam, NL)
  • Céline Kuttler (Lille I University, FR)
  • Pietro Lio (University of Cambridge, GB) [dblp]
  • Fei Liu (BTU Cottbus, DE) [dblp]
  • Wolfgang Marwan (Universität Magdeburg - IBIO, DE) [dblp]
  • Carsten Maus (Universität Rostock, DE) [dblp]
  • Ivan Mura (Microsoft Research - University Trento, IT)
  • Chris J. Myers (Univ. of Utah, US) [dblp]
  • Brett Olivier (Free University of Amsterdam, NL)
  • Alberto Policriti (University of Udine, IT)
  • Alessandro Romanel (ENS - Paris, FR)
  • Adelinde M. Uhrmacher (Universität Rostock, DE) [dblp]
  • Natal van Riel (TU Eindhoven, NL)
  • Bartek Wilczynski (University of Warsaw, PL)
  • Verena Wolf (Universität des Saarlandes, DE) [dblp]

Related Seminars
  • Dagstuhl Seminar 09091: Formal Methods in Molecular Biology (2009-02-22 - 2009-02-27) (Details)
  • Dagstuhl Seminar 14481: Multiscale Spatial Computational Systems Biology (2014-11-23 - 2014-11-28) (Details)

  • modelling
  • simulation / verification
  • logic / bioinformatics / interdisciplinary

  • Formal Modelling
  • Computational Systems Biology
  • Petri Nets
  • Process Algebra
  • Bioinformatics