Programme CMSB 2012

Proceedings available as: Springer LNCS.LNBI 7605 


Regular paper presentations: 30 minutes

Flash poster presentations: 5 minutes 

Wednesday 3rd October




Welcome address


invited talk by Denis Noble

Modular (1) 

Franck Delaplace, Hanna Klaudel, Tarek Melliti and Sylvain Sené. Analysis of modular organisation of interaction networks based on asymptotic dynamics 

Coffee Break 

High Performance Modelling 

Miguel Ángel Martínez Del Amor, Ignacio Pérez Hurtado, Adolfo Gastalver Rubio, Anne Cathrine Elster and Mario De Jesús Pérez Jiménez. Simulation of Population Dynamics P systems on CUDA

Jole Costanza, Giovanni Carapezza, Claudio Angione, Pietro Lio' and Giuseppe Nicosia. Optimization, Sensitivity and Robustness Analysis in FBA modeling 

Aurélien Naldi, Pedro Monteiro and Claudine Chaouiya. Efficient handling of large signalling-regulatory networks by focusing on their core control

Evening Reception in the London Rooms (Royal Society)
Thursday 4th October

09.00 -12.30

invited talk by Peter Kohl

Modular (2) 

Mary Ann Blaetke, Monika Heiner and Wolfgang Marwan. Predicting Phenotype from Genotype Through Automatically Composed Petri Nets

Coffee break 

Case studies (1)

David Marco, Erin Scott, David Cairns, Andrea Graham, Judi Allen, Simmi Mahajan and Carron Shankland. Investigating co-infection dynamics through evolution of Bio-PEPA model parameters: a combined process algebra and evolutionary computing approach

Sriram Sankaranarayanan and Georgios Fainekos. Simulating Insulin Infusion Pump Risks by In-Silico Modeling of the Insulin-Glucose Regulatory System.

Ibuki Kawamata, Nathanael Aubert, Masahiro Hamano and Masami Hagiya. Abstraction of Graph-Based Models of Bio-Molecular Reaction Systems for Efficient Simulation



13.30- 16.30


Kirill Batmanov, Francois Lemaire, Celine Kuttler, Cedric Lhoussaine and Cristian Versari. Symmetry-based model reduction for approximate stochastic analysis

Alfonso Carta, Madalena Chaves and Jean-Luc Gouzé. A Simple Model to Control Growth Rate of Synthetic E. coli during the Exponential Phase: Model Analysis and Parameter Estimation.  Best Student Paper.

Maxime Folschette, Loïc Paulevé, Katsumi Inoue, Morgan Magnin and Olivier Roux. Concretizing the Process Hitting into Biological Regulatory Networks

Coffee break 

Abhishek Murthy, Md. Ariful Islam, Ezio Bartocci, Flavio Fenton, Scott Smolka and Radu Grosu. Bisimulation-Based Abstraction of Sodium-Channel Dynamics in Cardiac-Cell Models

Santiago Videla, Carito Guziolowski, Federica Eduati, Sven Thiele, Niels Grabe, Julio Saez-Rodriguez and Anne Siegel. Revisiting the Training of Logic Models of Protein Signaling Networks with a Formal Approach based on Answer Set Programming. Best Paper.


Flash presentations

(1) Joseph O. Dada and Pedro Mendes. ManyCell: A multiscale simulator for cellular systems

(2) Vashti Galpin. Modelling trafficking of proteins within the mammalian cell using Bio-PEPA

(3) Mary Ann Blaetke, Anna Dittrich, Monika Heiner, Fred Schaper and Wolfgang Marwan. JAK-STAT Signalling as Example for a Database-Supported Modular Modelling Concept

(4) Russ Harmer, Jean Krivine, Élise Laruelle, Cedric Lhoussaine, Guillaume Madelaine and Mirabelle Nebut. Models of Tet-On System with Epigenetic Effects

(5) Larisa Soldatova, Qian Gao and David Gilbert. Towards an Ontology of Biomodelling

(6) François Fages, Steven Gay and Sylvain Soliman. Inferring Reaction Models from ODEs

(7) Asta Laiho, András Király and Attila Gyenesei. GeneFuncster: a web tool for gene functional enrichment analysis and visualization

(8) Ilya Potapov and Evgenii Volkov. Effects of Molecular Noise on the Multistability in a Synthetic Genetic Oscillator 


Poster session (see below for list) & Reception drinks


Conference dinner (Royal Society)

Friday 5th October


invited talk by Boris Kholodenko


Hannes Klarner, Juraj Kolčák, Adam Streck, David Šafránek and Heike Siebert. Parameter Identification and Model Ranking of Thomas Networks

Coffee break 

Case studies (2) 

Ilya Potapov, Jarno Mäkelä, Olli Yli-Harja and Andre Ribeiro. Sequence Dependent Properties of the Expression Dynamics of Genes and Gene Networks

Paolo Ballarini, Jarno Makela and Andre Ribeiro. Expressive Statistical Model Checking of Genetic Networks with Delayed Stochastic Dynamics

Laura Bennett, Artem Lysenko, Lazaros Papageorgiou, Martin Urban, Kim Hammond-Kosack, Chris Rawlings, Mansoor Saqi and Sophia Tsoka. Detection of multi-clustered genes and community structure for the plant pathogenic fungus Fusarium graminearum

12.30-13.30 onwards

Lunch in the Marble Hall

CMSB 2012 Accepted Regular Posters

(9) Elodie Ruelle, Luc Delaby, Michael Wallace and Laurence Shalloo. Developing a Cattle Model for Dairy Cows
(10) Noorie Karimbocus, Lin Li, Shan He and John K Heath. Modelling the Ras GTPase cycle using the Stochastic Pi Machine
(11) Dicle Hasdemir, Johan A. Westerhuis and Age K. Smilde. Exploring the Conditions for the Validity of Kinetic Metabolic Models
(12) Jeremie Bourdon, Damien Eveillard and Anne Siegel. Integrating qualitative and quantitative knowledge within a probabilistic framework: application to gene regulatory and metabolic reaction networks
(13) Vikash Pandey, Jian Li, Alexander Kühn, Hans Lehrach and Christoph Wierling. Comparative Evaluation of ODE- and Petri Net-Based Monte Carlo Simulation of Cellular Systems
(14) Peter Rashkov. Modeling a protein oscillator in bacteria
(15) Carolyn Talcott, Merrill Knapp and Tim McCarthy. A Knowledge Base of Curated Evidence for Cellular Signaling Networks
(16) David Šafránek, Jan Červený, Matej Klement, Luboš Brim, Dušan Lazár and Ladislav Nedbal. E-photosynthesis: Web-based platform for photosynthetic processes
(17) Tanya Curtis, Nigel Halford, Qian Gao and David Gilbert. Modelling asparagine synthetase function in wheat using Petri nets
(18) Kate Byrne, Lan Nguyen, Walter Kolch, Naser Monsefi, Alex von Kriegsheim and Boris Kholodenko. Bistability in the Rac1, PAK and RhoA network governs cancer cell motility.
(19) Aimee Carmody, Alex Cheong, Till D Frank, Walter Kolch and Boris N Kholodenko. Dissecting impacts of multiple transcription factors on c-fos proto-oncogene expression.

(20) Chris Banks and Ian Stark. A logic of behaviour in context

(21) Elisa Domínguez Hüttinger and Reiko J. Tanaka. Multi-scale modelling of epithelium regulation

(22) Dennis Lee, Hong Yue, Jun Yu and Stephen Marshall. Elucidating General Gene Network Component Activity using the NF-kB Pathway