Published: 8th September 2011
DOI: 10.4204/EPTCS.67
ISSN: 2075-2180


Proceedings Third International Workshop on
Computational Models for Cell Processes
Aachen, Germany, September 10, 2011

Edited by: Ion Petre and Erik de Vink

Ion Petre and Erik de Vink
Invited Presentation: Parameter Estimation for Stochastic Models of Chemical Reaction Networks
Verena Wolf
Invited Presentation: Spatial modeling and simulation in cell biology
Adelinde M. Uhrmacher
Modelling Spatial Interactions in the Arbuscular Mycorrhizal Symbiosis using the Calculus of Wrapped Compartments
Cristina Calcagno, Mario Coppo, Ferruccio Damiani, Maurizio Drocco, Eva Sciacca, Salvatore Spinella and Angelo Troina
Programmable models of growth and mutation of cancer-cell populations
Luca Bortolussi and Alberto Policriti
A semi-quantitative equivalence for abstracting from fast reactions
Vashti Galpin, Jane Hillston and Federica Ciocchetta
A Minimal OO Calculus for Modelling Biological Systems
Livio Bioglio
A Study of the PDGF Signaling Pathway with PRISM
Qixia Yuan, Jun Pang, Sjouke Mauw, Panuwat Trairatphisan, Monique Wiesinger and Thomas Sauter
Multiple verification in computational modeling of bone pathologies
Pietro Liò, Emanuela Merelli and Nicola Paoletti
Reachability in Biochemical Dynamical Systems by Quantitative Discrete Approximation (extended abstract)
L. Brim, J. Fabriková, S. Dražan and D. Šafránek


The third international workshop on Computational Models for Cell Processes (CompMod 2011) took place on September 10, 2011 at the University of Aachen, Germany, in conjunction with CONCUR 2011. The first edition of the workshop (2008) took place in Turku, Finland, in conjunction with Formal Methods 2008 and the second edition (2009) took place in Eindhoven, the Netherlands, as well in conjunction with Formal Methods 2009. This volume contains the final versions of all contributions accepted for presentation at the workshop.

The goal of the CompMod workshop series is to bring together researchers in Computer Science (especially in Formal Methods) and Mathematics (both discrete and continuous), interested in the opportunities and the challenges of Systems Biology. CompMod 2011 has received 8 submissions, authored by 28 different authors from 6 different countries. All papers were of high scientific level and the Program Committee selected 7 papers for presentation at the workshop. We thank the PC members for their excellent work in making this selection. The CompMod 2011 Program Committee consisted of:

The scientific program of the workshop spans an interesting mix of approaches to systems biology, ranging from quantitative to qualitative techniques, from continuous to discrete mathematics, and from deterministic to stochastic methods. We thank our invited speakers

for accepting our invitation and for presenting some of their recent results at CompMod 2011 on inference algorithms for data extraction and subsequent model adaptation, and on modeling and simulation of inter-compartment and cross-membrane phenomena using rule-based languages. The technical contributions address process algebraic treatment of plant-fungus symbiosis using explicit spatial labeling in the Calculus of Wrapped Compartments, comparison of therapy strategies for prostate cancer growth using the stochastic modeling language sCCP augmented with events and random updates, a notion of semi-quantitative equivalence in the context of biological modeling with fast and slow reactions for the Bio-PEPA language, a core rewrite calculus bringing object-oriented concepts to biological ontologies, a probabilistic analysis of the PDGF signaling pathway using the PRISM model checker the interpretation of osteoporosis as a defective bone remodeling dynamics and related diagnostic estimators, and a resolution dependent approximation of continuous dynamical systems for reachability analysis in systems biology. Similarly as for the past two editions of CompMod, a special issue of the LNBI Transactions on Computational Systems Biology (Springer) will be based on CompMod 2011. The forthcoming special issue will have a separate, open call for papers following the workshop in Aachen and all submissions will be subject to a separate review process. We would also like to thank the editorial board of the Electronic Proceedings in Theoretical Computer Science (EPTCS) for accepting to publish these proceedings in their series.

Ion Petre, Erik de Vink

Turku, Finland and Eindhoven, the Netherlands, August 2011

Workshop organizers and PC co-chairs

Parameter Estimation for Stochastic Models of Chemical Reaction Networks

Verena Wolf (Saarland University, Saarbrücken, Germany)

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.

Spatial modeling and simulation in cell biology

Adelinde M. Uhrmacher (University of Rostock, Germany)

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.