What are the salient features of the new scientific context within which biological modelling and simulation will evolve from now on? The global project of high-throughput biology may be summarized as follows. After genome sequencing comes the annotation by 'classical' bioinformatics means. It then becomes important to interpret the annotations, to understand the interactions between biological functions, to predict the outcome of perturbations, while incorporating the results from post genomics studies (of course, sequencing and annotation do not stop when simulation comes into the picture). At that stage, a tight interplay between model, simulation and bench experimentation is crucial. Taking on this challenge therefore requires specialists from across the sciences to learn each other's language so as to collaborate effectively on defined projects. This book gathers overviews of the talks, original articles contributed by speakers and subgroups, tutorial material, and poster abstracts. We thank the sponsors of this conference for making it possible for all the participants to share their enthusiasm and ideas in such a constructive way.