April 10 – 15 , 2011, Dagstuhl Seminar 11151

Formal Methods in Molecular Biology


Rainer Breitling (University of Manchester, GB)
Frank J. Bruggeman (CWI – Amsterdam, NL)
Corrado Priami (Microsoft Research – University Trento, IT)
Adelinde M. Uhrmacher (Universität Rostock, DE)

The Dagstuhl Foundation gratefully acknowledges the donation from:

  •   Microsoft Research, Cambridge, UK

For support, please contact

Dagstuhl Service Team


Dagstuhl Report, Volume 1, Issue 4 Dagstuhl Report
List of Participants
Dagstuhl Seminar Schedule [pdf]


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').

Dagstuhl Seminar Series


  • Modelling
  • Simulation / Verification
  • Logic / Bioinformatics / Interdisciplinary


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


In the series Dagstuhl Reports each Dagstuhl Seminar and Dagstuhl Perspectives Workshop is documented. The seminar organizers, in cooperation with the collector, prepare a report that includes contributions from the participants' talks together with a summary of the seminar.


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