CompMod 2009

2nd International Workshop on Computational Models for Cell Processes

November 3, 2009 , Eindhoven, the Netherlands

In conjunction with Formal Methods 2009

Technische Universiteit Eindhoven, Eindhoven, the Netherlands


Systems Biology is an exciting new application area for computer science. This workshop of FM 2009 fosters an excellent platform gathering researchers in formal methods and related fields that are interested in the wealth of opportunities and challenges in systems biology. In particular, we welcome contributions that address both theoretical and applied contributions related to the relevance and potential of formal methods in biology. Of special interest are contributions that present biological processes requiring special tools and techniques that have not been investigated so far in the context of formal methods, as well as extensions of formal methods formalisms introduced to improve their applicability to biology. Topics of interest include, but are not limited to:


Call for papers


We seek original contributions on the topics of the workshop. Authors are invited to submit extended abstracts or full papers of up to 15 pages formatted according to EPTCS guidelines. Electronic submissions should be formatted in PDF. Simultaneous submission to other conferences or workshops with published proceedings is not allowed. All submissions will be peer-reviewed and discussed within the programme committee. The proceedings of the workshop will be published in the new series of Electronic Proceedings in Theoretical Computer Science. A special issue of a high-level international journal, based on the workshop, is planned after the workshop.

Manuscripts can be uploaded online at


The proceedings of CompMod2009 are published by EPTCS and are available from DOI: 10.4204/EPTCS.6




  08.50 - 09.00 Ion Petre Opening
Session 1. (Chair: R.Back)
  09.00 - 09.50 J. Fisher The executable pathway to biological networks
  09.50 - 10.15 L.Loewe, S.Moodie, J.Hillston Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA
  10.15 - 10.45 Coffee break  
Session 2 (Chair E. de Vink)
  10.45 - 11.10 L.Bortolussi, A.Policriti Hybrid semantics of stochastic programs with dynamic reconfiguration
  11.10 - 11.35 D.Besozzi, P.Cazzaniga, M.Dugo, D.Pescini, G.Mauri A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis
  11.35 - 12.00 R.Barbuti, G.Caravagna, A.Maggiolo Schettini, P.Milazzo On the interpretation of delays in delay stochastic simulation of biological systems
  12.00 - 13.30 Lunch  
Session 3 (Chair: I. Petre)
  13.30 - 13.55 M.Coppo, F.Damiani, E.Grassi, M.Guether, A.Troina Modelling an ammonium transporter with SCLS
  13.55 - 14.20 B.Aman, G.Ciobanu Mobile membranes with timers
  14.20 - 14.45 H.Siebert Dynamical and structural modularity of discrete regulatory networks
  14.45 - 15.15 Coffee break  
Session 4 (Special session in collaboration with the EC-MOAN project; Chair: J. van de Pol)
  15.15 - 15.40 J. van de Pol Overview of the EC-MOAN project
  15.40 - 16.30 H. de Jong Qualitative modeling and simulation of bacterial regulatory networks
  16.30 - 16.55 J.Barnat, L.Brim, I.Cerna, S.Drazan, J.Fabrikova, J. Lanek, D.Safranek, H. Ma BioDiVinE: a framework for parallel analysis of biological models
  16.55 - 17.00 I.Petre Closing
  19.00 - XX.XX Dinner Restaurant Indonesia, Jan van Lieshoutstraat 22, near the Market square. The cost is included in the participation fee.


Important dates


Submission: July 15, 2009
Notification: September 10, 2009
Final version: October 1, 2009
Workshop: November 3, 2009



Invited speakers


Jasmin Fisher, Microsoft Research Cambridge, jasmin.fisher 'AT'

Hidde de Jong, INRIA Grenoble - Rhône-Alpes, 'AT'

Grzegorz Rozenberg, University of Leiden, rozenber 'AT' - cancelled


Titles and abstracts of the invited talks are here.


Programme committee




Organizing committee





For registration use the dedicated page of FM'2009 at and follow the link "Registration".






The workshop will be held in Eindhoven at the campus of the Eindhoven University of Technology.

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