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SELECTBIO Conferences Informatics

Informatics Agenda

Other Track Agendas

Cancer Proteomics | Exosomes and Markers in Biological Fluids | Informatics | Metabolic Profiling & Lipidomics | 

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Tuesday, 16 October 2012




Pedro MendesKeynote Presentation

Towards Whole-Genome Kinetic Models of Metabolism
Pedro Mendes, Professor in Computational Systems Biology, The University of Manchester, United Kingdom

Latest developments in the methodology to construct whole-genome kinetic models of metabolism will be presented. Issues include thermodynamic constraints and parameter estimation.

Frameworks and Techniques for Verifying, Validating, Analyzing, and Simulating Biological Systems


CANCELLED - Anatomy of Parallel Stochastic Simulation of Biological Networks
Tommaso Mazza, Bioinformatics Unit Head, Casa Sollievo della Sofferenza, Italy


Coffee Break & Networking in Exhibition Hall


A New Framework to Analyze Huge Biological Regulatory Networks
Olivier Roux, Professor of Computer Science, Ecole Centrale de Nantes, France


Identifying the Optimal Model to Represent Biochemical Systems
Mochamad Apri, Research Scientist, Wageningen University and Research Centre, Netherlands

We present a novel method to extract an optimal model from the full model to represent biochemical systems. The resulting model contains only important components and parameters that are necessary to govern dynamics of the system in any allowed conditions.


Lunch & Networking in Exhibition Hall


Poster Viewing Session


Analysing Molecular Networks using Probabilistic Model Checking: From Signalling Pathways to Molecular Programming
Marta Kwiatkowska, Professor, University of Oxford, United Kingdom

The lecture will give a brief introduction to probabilistic model checking and PRISM (, and then demonstrate how to apply it, first to model and analyse signalling pathways, and then how to detect and correct flaws in DNA device designs.

Informatics and Cancer


Investigating & Predicting Cancer Mutations Using Protein Interfaces
Octavio Espinosa, PostDoc, The Institute of Cancer Research, United Kingdom

Recent analyses on protein crystal structures in the Protein Data Bank Europe have revealed a comprehensive set of protein interfaces. Coupled with the comprehensive mutation data from NGS, this gives the possibility of exploring how mutations have structural effects on proteins and, therefore, useful insights into how such mutations may contribute to the phenotype of cancer genomes.


Coffee Break & Networking in Exhibition Hall

Model Integration and Reduction Methods


Formal Model Reduction
Jerome Feret, Research Fellow, INRIA, France

Rule-based modeling provides a very compact representation for protein-protein interaction networks, which emphasizes the biochemical structure of chemical complexes. We track the flow of information throughout these biochemical structures so as to deduce a coarse-graining of the underlying ODE systems.


Which Details Matter? Model Reduction Helps Computational Biology
Ovidiu Radulescu, Professor, Université de Montpellier, France

We show how to obtain multiscale simplifications of biochemical reaction networks used for modeling  cell physiology. Model reduction provides strategies to extract the essential features of a complex model and use them for model identification and model analysis.


Drinks Reception

Wednesday, 17 October 2012


Weida TongKeynote Presentation

Regulatory Science – A Drug Development Perspective
Weida Tong, Director, US Food and Drug Administration, United States of America

In this presentation I will explain the FDA's new initiative on advancing regulatory science and its implication on drug development.  Three paradigms to enhance the drug pipeline will also be discussed, along with three projects in FDA relating drug development via regulatory science.  


Coffee Break and Networking

High-Performance Computational Systems Biology and Parallel Running


Petri Nets for Systems Biology
Ina Koch, Professor of Bioinformatics, University of Frankfurt, Germany

Petri net formalism provides useful methods for systems biology. The talk explains the application of Petri nets using biochemical examples. For intuitive understanding, basic foundations of Petri nets will be introduced. Scope and limits of the method will be discussed.


Lunch, Poster Viewing and Networking


Computational Prediction and Analysis of Metabolism in Tissue and Cells During Disease Progression
Hans van Beek, Computational Systems Biologist , Vanderbilt University Medical Center, Netherlands

Metabolic patterns in diseased brain are predictable from gene expression and metabolite uptake. Metabolism is measured in tissue biopsies and cell cultures. Computational models show adaptation and failure of energy fluxes in cells and whole body under stress.


Modelling and Methods to Control the Field of Activation for Deep Brain Stimulation
Richard Bayford, Professor, Middlesex University, United Kingdom

This presentation describes the development of methods to model the electrical field in the human head and achieve better selectivity and electric field shifting during deep brain stimulation. 


Coffee Break and Networking

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