CMSB
2014

Conference Programme

List of accepted papers and poster abstracts.

The conference proceedings have now been published as a volume 8859 in the Lecture Notes in Bioinformatics series.

Final Schedule

	Monday, 17th November
9:00–9:25	Registration and coffee
9:25–9:30	Welcome Address
9:30–12:00	Session 1: Frameworks for model verification, validation, and analysis of biological systems Chair: Carolyn Talcott Rosario Distefano, Dynamic modeling and simulation of leukocyte integrin activation through an electronic design automation framework. Pauline Traynard, Trace simplification for temporal logic constraint solving: Application to oscillation constraints between the circadian clock and the cell cycle. Loïc Paulevé, Characterization of reachable attractors using Petri net unfoldings. Nicola Paoletti, Precise parameter synthesis for stochastic biochemical systems. Paolo Zuliani Parameter synthesis for cardiac cell hybrid models using δ-decisions.
12:00–13:30	Lunch
13:30–14:00	Poster Flashes Chair: Joseph Dada Jean-Loup Faulon, XTMS in action: retrosynthetic design in the extended metabolic space of heterologous pathways for high-value compounds Abhishekh Gupta, Modelling Polar Retention of Complexes in Escherichia coli Argyris Zardilis, Extensible and Executable Stochastic Models of Fatty Acid and Lipid Metabolism Donal Stewart, FM-Sim: Protocol Definition, Simulation and Rate Inference for Neuroscience Assays Arne T. Bittig, Predictive Modelling of Mitochondrial Spatial Structure and Health Natasa Miskov-Zivanov, THiMED: Time in Hierarchical Model Extraction and Design
14:00–15:00	Invited Speaker: Ruth Baker, University of Oxford "Experimental and Modelling Investigation of Monolayer Development with Clustering" Chair: Kieran Smallbone
15:00–15:30	Coffee break
15:30–17:30	Session 2: Models and their biological applications Chair: François Fages Eugenio Cinquemani, Towards real-time control of gene expression at the single cell level: a stochastic control approach. Agnes Köhler, A rule-based model of base excision repair. Rachel Lintott, Using process algebra to model radiation induced bystander effects. Rafael Costa, Exploring the Cellular Objective in Flux Balance Constraint-Based Models.
17:30–18:00	Business meeting
17:45–19:00	Reception

	Tuesday, 18th November
9:00–10:00	Invited Speaker: Dagmar Iber, ETH Zürich "From Networks to Function—Computational Models of Organogenesis" Chair: Pedro Mendes
10:00–10:30	Coffee break
10:30–10:35	Announcement of CMSB 2015 (Carito Guziolowski)
10:35–12:05	Session 3: Model inference from experimental data Chair: Ursula Kummer Fabian Fröhlich, Radial basis function approximation of Bayesian parameter posterior densities for uncertainty analysis. Attila Gábor, Improved Parameter Estimation in Kinetic Models: Selection and Tuning of Regularization Methods. Fabian Fröhlich, Uncertainty analysis for non-identifiable dynamical systems: profile likelihoods, bootstrapping and more.
12:00–13:30	Lunch
13:30–14:00	Session 4: Computational approaches for synthetic biology Chair: Reinhard Laubenbacher Julio R. Banga, Optimization based design of synthetic oscillators from standard biological parts.
14:00–15:30	Poster session (with coffee) list of accepted posters Posters must be smaller than A1 size (59.4 x 84.1 cm / 23.4 x 33.1 inches)
15:30–17:00	Social event: Visit to the Museum of Science and Industry (MoSI) At MoSI we will see a live demonstration of the Baby, the world's first stored-program electronic digital computer. It was first successfully operated in June 1948 running a program to factorize 218. This is the computer that gave birth to software, and was also responsible for Alan Turing to move to Manchester.
18:30 —	Conference dinner at EastZEast Riverside.

	Wednesday, 19th November
9:00–10:00	Invited Speaker: Magnus Rattray, University of Manchester "Integrating mRNA and Polymerase Time Course Data to Model the Dynamics of Transcription" Chair: Pedro Mendes
10:00–10:30	Coffee break
10:30–12:00	Session 5: Formalisms for modelling biological processes Chair: Julio R. Banga Sabine Peres, SAT-based metabolics pathways analysis without compilation. Alexandre Temperville, On defining and computing "good" conservation laws. Kirsten Thobe, Model integration and crosstalk analysis of logical regulatory networks.
12:00–12:10	Closing remarks
12:10 —	Packed lunch available for those who sign up.

The conference proceedings were published in Springer's Lecture Notes in Bioinformatics, volume 8859. A free copy will be supplied, at the conference, to all the participants