Computational Models for Cell Processes

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:

Formal models for cellular pathways
Qualitative biological modeling
Quantitative formal methods
Theoretical comparison of formalisms for biological processes
Biologically-inspired extensions to formal methods, concurrency theory, or logical methods
Differential, discrete and/or stochastic modeling languages
Reconstruction of biological networks based on empirical data
Decomposition and modularization of large biological networks
Applications of formal methods and computational modeling
Membrane systems as a modeling platform

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 http://www.easychair.org/conferences/?conf=compmod2009.

Proceedings

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

Program

	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' microsoft.com

Hidde de Jong, INRIA Grenoble - Rhône-Alpes, Hidde.de-Jong 'AT' inria.fr

Grzegorz Rozenberg, University of Leiden, rozenber 'AT' liacs.nl - cancelled

Titles and abstracts of the invited talks are here.

Programme committee

Ralph-Johan Back, Åbo Akademi, Finland
Luboš Brim, Masaryk University, Czech Republic
Muffy Calder, University of Glasgow, UK
Eugen Czeizler, Åbo Akademi, Finland
Vincent Danos, University of Edinburgh, UK
Russ Harmer, University of Paris 7, France
Monika Heiner, Brandenburg University of Technology Cottbus, Germany
Jane Hillston, University of Edinburgh, UK
Ina Koch, Max Planck Institute for Molecular Genetics, Germany
Vincenzo Manca, Università di Verona, Italy
Giancarlo Mauri, Università Degli Studi di Milano-Bicocca, Italy
Satoru Miyano, University of Tokyo, Japan
Andrei Pãun, Louisiana Tech University, US
Ion Petre, Åbo Akademi, Finland
Jaco van de Pol, University of Twente, the Netherlands
Alberto Policriti, Università di Udine, Italy
Erik de Vink, Eindhoven University of Technology, the Netherlands

Organizing committee

Ion Petre:
Ralph-Johan Back:
Erik de Vink:

Registration

For registration use the dedicated page of FM'2009 at http://www.win.tue.nl/fm2009/ and follow the link "Registration".

Location

Venue:

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

Related Events:

Tutorial on "Computational Systems Biology", November 2, 2009, Technical University of Eindhoven, the Netherlands.
Formal Methods 2009, November 2-8, 2009, Technical University of Eindhoven, the Netherlands.
Previous Edition, May 27, 2008, Turku, Finland.