3rd International Workshop on Computational Models for Cell Processes

CompMod 2011

September 10, 2011, Aachen, Germany

In conjunction with CONCUR 2011

University of Aachen, Germany

Systems Biology is an exciting new application area for computer science. This workshop of CONCUR 2011 fosters an excellent platform gathering researchers in concurrency theory, formal methods, and related fields that are interested in the wealth of opportunities and challenges in systems biology. 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 series of Electronic Proceedings in Theoretical Computer Science. A special issue of Transactions on Computational Systems Biology, based on the workshop, is planned after the workshop.

Manuscripts can be uploaded online at http://www.easychair.org/conferences/?conf=compmod2011.

Program

  09.00 - 10.00 Session 1
  Verena Wolf Parameter Estimation for Stochastic Models of Chemical Reaction Networks (invited talk)
 
  10.10 - 10.30 Coffee break  
 
  10:30-12:00 Session 2
  Cristina Calcagno, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella and Angelo Troina Modelling Spatial Interactions in the Arbuscular Mycorrhizal Symbiosis using the Calculus of Wrapped Compartments
  Luca Bortolussi and Alberto Policriti Programmable models of growth and mutation of cancer-cell populations
  Vashti Galpin, Jane Hillston and Federica Ciocchetta A semi-quantitative equivalence for abstracting from fast reactions
 
  12.00 - 14.00 Lunch  
 
  14:00-16:00 Session 3
  Adelinde Uhrmacher Spatial modeling and simulation in cell biology (invited talk)
  Livio Bioglio A Minimal OO Calculus for Modelling Biological Systems
  Qixia Yuan, Jun Pang, Sjouke Mauw, Panuwat Trairatphisan, Monique Wiesinger and Thomas Sauter A Study of the PDGF Signaling Pathway with PRISM
 
  16.00 - 16:30 Coffee break  
 
  16.30-17.30 Session 4
  Pietro Liò , Emanuela Merelli and Nicola Paoletti Multiple verification in computational modeling of bone pathologies
  Luboš Brim, Jana Fabrikovà, Sven Dražan and David Safranek Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation

Important dates

Invited speakers

Adelinde Uhrmacher, University of Rostock, Germany

Spatial modeling and simulation in cell biology

Spatial phenomena from shuttling of proteins between compartments, diffusion of proteins within cell compartments, reactions at and within the membranes, and excluded volume effects are receiving increasingly attention in cell biological modeling and simulation. We will explore how these phenomena can be described in rule-based languages, discuss what kind of implications this has for the semantics, and for the efficiency of simulations. The difficulty of designing and evaluating efficient simulators will be illuminated based on an extensive performance study on spatial Gillespie-type simulators.

Verena Wolf, Saarland University, Germany

Parameter Estimation for Stochastic Models of Chemical Reaction Networks

The calibration of mathematical models using wet-lab data is an important part of systems biology research, since many models are initially designed on the basis of hypotheses and literature search. As the measurements of molecule counts in single cells are becoming more accurate, stochastic models can be accurately adjusted. For this, computationally expensive inference algorithms are necessary to extract as much information as possible from the data and to fit the model accordingly. In this talk I will present several numerical approaches to parameter inference for stochastic models of chemical reaction networks. Measurements in equilibrium and during the transient phase will be considered as well as data with measurement errors.

Programme committee

 

Organizing committee

Ion Petre (Åbo Akademi University, Finland):
Erik de Vink (Eindhoven University of Technology, the Netherlands):

Location

COMPMOD 2011 will take place at University of Aachen, Germany, as a satellite event to the 22nd International Conference on Concurrency Theory 2011 (CONCUR 2011).

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