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Dr Hugo Van den Berg, University of Warwick
Biography
Hugo van den Berg graduated cum laude from the Free University in Amsterdam in 1992, earning an MSc in theoretical neuroscience. In 1998 he obtained a PhD at the same University in theoretical population biology and became a Research Fellow at the University of Warwick, where he started working on the specificity of T cell receptors. His other research interests include myometrial activity patterns and whole-body energetics.
Mike Holcombe, The University of Sheffield
Abstract
We will look at new techniques for simulating complex systems using agent-based models and supercomputers. The FLAME (Flexible Large-scale Agent-based Modelling Environment) has been developed following rigorous software engineering best practice to provide an environment where researchers can build highly detailed and robust models. FLAME is a program generator that starts with a specification of all the different agent types in a Multi-agent system and directly produces a highly optimised C program that will run on any computer system - desktop, Grid, parallel supercomputer etc. It is also available for GPGPUs for graphics-intensive applications. The basis of FLAME is a fully general computational model and thus it is applicable to many situations in biology, medicine, economics and social systems, for example. FLMAE can be integrated with other applications and solvers, for example COPASI used in mathematical and systems biology (it is SBML compliant). We will look at how to engineer massive agent-based systems using FLAME and the associated techniques for model testing, model validation and verification. techniques for automatically discovering emergent phenomena from massive data sets produced by these simulations will also be mentioned. Examples will be drawn from: models of the innate immune system in mammallian cells, models of the molecular basis for oxygen processing in E. coli and the development and repair of epithelial tissue.