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Modelling Evolutionary Biology

22 February 2016

High performance computing (HPC) is increasingly critical to evolutionary biology research.  Biologists at University of Sydney are intensive users of the HPC services through Intersect.  ARC Future Fellow Professor Madeleine Beekman and her university colleagues use hundreds of thousands of service units per year to do their computer simulation.  Three areas of their research where HPC is essential for modeling are in rapid development: evolution of virulence, genome evolution and collective animal behaviour.  

In the field of animal behaviour, acts of coordinated collective motion arise in groups that can range in size from a few to tens of thousands. Modelling such behaviours reveals many important things, such as how members of species interact under predation, how they manage resources more collectively, and at the same time provide biological analogues for future robotics control. Each simulation time-step includes an Ο(N2) calculation, and needs to be run across many steps and models.  It takes around eight hours on several central processing units (desktop computers)  just to accurately model a group of eight fish swimming in an annular tank for a few minutes.  Therefore greater processing speed, memory and a larger numbers of processors make simulation of realistically large groups of animals in motion a practical reality.  

HPC is crucial for research in evolutionary biology to advance.