EPTCS 6
Proceedings Second International Workshop on
Computational Models for Cell Processes
Eindhoven, the Netherlands, November 3, 2009
Edited by: Ralph-Johan Back, Ion Petre and Erik de Vink
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Preface
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Mutual Mobile Membranes with Timers
Bogdan Aman and Gabriel Ciobanu | 1 |
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On the Interpretation of Delays in Delay Stochastic Simulation of Biological Systems
Roberto Barbuti, Giulio Caravagna, Paolo Milazzo and Andrea Maggiolo-Schettini | 17 |
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BioDiVinE: A Framework for Parallel Analysis of Biological Models
Jiří Barnat, Luboš Brim, Ivana Černá, Sven Dražan, Jana Fabriková, Jan Láník, David Šafránek and Hongwu Ma | 31 |
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A study on the combined interplay between stochastic fluctuations and the number of flagella in bacterial chemotaxis
Daniela Besozzi, Paolo Cazzaniga, Matteo Dugo, Dario Pescini and Giancarlo Mauri | 47 |
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Hybrid Semantics of Stochastic Programs with Dynamic Reconfiguration
Luca Bortolussi and Alberto Policriti | 63 |
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Modelling an Ammonium Transporter with SCLS
Mario Coppo, Ferruccio Damiani, Elena Grassi, Mike Guether and Angelo Troina | 77 |
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Quantifying the implicit process flow abstraction in SBGN-PD diagrams with Bio-PEPA
Laurence Loewe, Stuart Moodie and Jane Hillston | 93 |
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Dynamical and Structural Modularity of Discrete Regulatory Networks
Heike Siebert | 109 |
Computational Models for Cell Processes (CompProc 2009)
The second international workshop on Computational Models
for Cell Processes (ComProc 2009)
took place on November 3, 2009 at the Eindhoven University of Technology, in conjunction with
Formal Methods 2009. The first edition of the workshop (2008)
took place in Turku, Finland, in conjuction with Formal Methods 2008.
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 2009 has received 19 submissions, authored by 60 different authors from
7 countries. Most authors came from Italy (26), UK (11), and the Netherlands (11).
The Program Committee has selected 8 papers for presentation at the workshop.
We thank the PC members for their excellent work in making this selection. The CompMod 2009
Program Committee consisted of:
- Ralph-Johan Back (Abo Akademi University, Finland) Co-Chair
- Lubos Brim (Masaryk University, Czech Republic)
- Muffy Calder (University of Glasgow, UK)
- Eugen Czeizler (Abo Akademi University, Finland)
- Vincent Danos (University of Edinburgh, UK)
- Russ Harmer (University of Paris 7, France)
- Monika Heiner (Brandeburg University of Technology Cottbus, Germany)
- Jane Hillston (University of Edinburgh, UK)
- Ina Koch (Max Planck Institute for Molecular Genetics, Germany)
- Vincenzo Manca (Universita di Verona, Italy)
- Giancarlo Mauri (Universita Degli Studi di Milano-Bicocca, Italy)
- Satoru Miyano (University of Tokio, Japan)
- Andrei Paun (Louisiana Tech University, US)
- Ion Petre (Abo Akademi University, Finland) Co-Chair
- Jaco van de Pol (University of Twente, the Netherlands)
- Alberto Policriti (Universita di Udine, Italy)
- Erik de Vink (Eindhoven University of Technology, the Netherlands) Co-Chair
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 three invited speakers
- Jasmin Fisher (Microsoft Research Cambridge, UK)
- Hidde de Jong (INRIA Grenoble-Rhone-Alpes, France)
- Grzegorz Rozenberg (Leiden, the Netherlands; Boulder, Colorado, US)
for accepting our invitation and for presenting some of their recent results at CompMod 2009.
Similarly as last year, a special issue of LNBI Transactions on
Computational Systems Biology (Springer) will be based on CompMod 2009. The forthcoming special issue
will have a separate, open call for papers in early 2010 and all submissions will be subject
to a separate review process.
This edition of CompMod was jointly organized with the EC-MOAN
project. We have organized a special session of the workshop dedicated to the project,
where a brief overview of EC-MOAN was presented, together with the invited talk by Hidde de Jong
(a member of the project), and a contributed paper by members of EC-MOAN. We are grateful
to Jaco van de Pol and to Lubos Brim for agreeing to collaborate with us on the workshop. We also
thank FME for their financial support.
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.
Ralph-Johan Back, Ion Petre, Erik de Vink
Turku, Finland and Eindhoven, the Netherlands, October 2009
Workshop organizers and PC co-chairs