My research interests are in the field of Scientific and High Performance Computing. The core of my PhD research has been the development of new numerical and computational techniques for multiscale Systems Biology simulation, and specifically multiscale simulations of human ventricular electrophysiology. I have been one of the leading developers of the first open source package for Systems Biology simulation: Chaste (www.cs.ox.ac.uk/chaste). My work has been pivotal in speeding up the Chaste cardiac solver by 3 orders of magnitude since I joined the project. This improvement has come through the successful application of domain decomposition techniques, investigation of better preconditioning for Krylov subspace iterative methods, as well as analysis and minimisation of communication in the underlying Finite Element Method solver and I/O optimisation. Thanks to that speed up, I can now run computationally very demanding simulations of the electrical activity in the human heart using patient-specific anatomical meshes and cutting-edge HPC infrastructures such as HECToR (UK's high-end computational resource). I am currently interested in the adoption of professional software engineering techniques for the development of software in academia as a way of making research long-lasting and reproducible. I am also interested in understanding the challenges posed by the new generation of peta/exascale and manycore architectures in terms of the design of new numerical techniques and parallel algorithms that will enable simulation across the scientific spectrum.
For a complete list of my publications see my CV.
Ten simple rules for effective computational research
J.M. Osborne‚ M.O. Bernabeu‚ M. Bruna‚ B. Calderhead‚ J. Cooper‚ N. Dalchau‚ S−J. Dunn‚ A.G. Fletcher‚ R. Freeman‚ D. Groen‚ B. Knapp‚ G.J. McInerny‚ G.R. Mirams‚ J. Pitt−Francis‚ B. Sengupta‚ D.W. Wright‚ C.A. Yates‚ Gavaghan D.J.‚ S. Emmott and C. Deane
In PLoS Computational Biology. Vol. 10. No. 3. Pages e1003506. 2014.
Chaste: an open source C++ library for computational physiology and biology
G.R. Mirams‚ C.J. Arthurs‚ M.O. Bernabeu‚ R. Bordas‚ J. Cooper‚ A. Corrias‚ Y. Davit‚ S−J. Dunn‚ A.G. Fletcher‚ D.G. Harvey‚ M.E. Marsh‚ J. M. Osborne‚ P. Pathmanathan‚ J. Pitt−Francis‚ J. Southern‚ N. Zemzemi and D.J. Gavaghan
In PLoS Computational Biology. Vol. 9. No. 3. Pages e1002970. 2013.
Computational assessment of drug−induced effects on the electrocardiogram: from ion channel block to body surface potentials
N Zemzemi‚ MO Bernabeu‚ J Saiz‚ J Cooper‚ P Pathmanathan‚ GR Mirams‚ J Pitt−Francis and B Rodriguez
In British Journal of Pharmacology. Vol. 168. No. 3. Pages 718−733. 2013.