Preface

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:

• Ralph-Johan Back Abo Akademi University, Finland
• Vincent Danos (University of Edinburgh, UK)
• Francois Fages (INRIA Paris-Rocquencourt, France)
• Russ Harmer (University of Paris 7, France)
• Monika Heiner (Brandenburg University of Technology Cottbus, Germany)
• Jane Hillston (University of Edinburgh, UK)
• Ina Koch (Goethe-University Frankfurt am Main, Germany)
• Giancarlo Mauri (Universita degli Studi di Milano-Bicocca, Italy)
• Emanuela Merelli (University of Camerino, Italy)
• Ion Petre (Abo Akademi University, Finland) Co-Chair
• Alberto Policriti (Universita di Udine, Italy)
• Corrado Priami (Microsoft Research -- University of Trento, Centre for Computational and Systems Biology, Italy)
• Angelo Troina (Universita degli Studi di Torino, Italy)
• Adelinde Uhrmacher (University of Rostock, Germany)
• Erik de Vink (TU Eindhoven, the Netherlands) Co-Chair

• Verena Wolf (Saarland University Saarbrucken, Germany)
• Adelinde Uhrmacher (University of Rostock, Germany)

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

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

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.