I am interested in applying computational methods to biological systems and problems. I am especially interested in general purpose computing on many-core systems like graphics processing engines (GPUs). My current work is on stochastic simulation of chemical reaction systems, especially biological systems, on CUDA-based GPUs. I am also working on threading strategies on GPUs.
My further interests are reverse-engineering of biochemical networks and global optimisation.
Software and Projects
STOCHSIMGPU is a MATLAB plugin computing stochastic simulations of chemical reaction systems in parallel on GPUs. The in Systems Biology most commonly used exact stochastic simulation algorithms SSA, LDM and NRM are implemented. The aim of STOCHSIMGPU is to enable the non-expert biologist to perform simulations on GPUs.
Fat vs thin threading explores a novel thin threading strategy on GPUs. Thin threads maximise parallelism to hide the access latency of global memory.
I am a fourth year Systems Biology DPhil student at Oxford University. I am a member of the Systems Biology Doctoral Training Centre and the Centre for Mathematical Biology. I studied computer engineering at the TU Hamburg-Harburg, Germany, and the University of Waterloo, Canada, and did a prost-graduate program at the University of Cologne and the German Cancer Research Center (DKFZ) in Heidelberg. I also hold an MBA in financial management. Before starting my DPhil, I have been working as a team leader and internal consultant in the telecommunications industry. My research is on the parallel stochastic simulation of biochemical reaction systems on massively parallel processors. My blog can be found here.