3D Optical Projection Tomography Microscopy Grid

HPC is becoming much more widely used in medical applications. The Optical Projection Tomography Microscopy Grid project was a collaboration between EPCC/NeSC and the MRC Human Genetics Unit to demonstrate the benefits of Grid technologies to biological research.

Modern biological research is data intensive and relies on an efficient informatics infrastructure. Research on the genetic control of embryo development involves large volume image data requiring significant computing resources for reconstruction, mapping and analysis. Technologies such as the Globus Toolkit and Sun Grid Engine can be used to deliver secure and transparent access to high performance computing to the laboratory workbench.

This project took an existing serial reconstruction code for Optical Projection Tomography, a new technique developed by the HGU, parallelised it using MPI, deployed it using Sun Grid Engine, and produced a Grid version utilising the Globus Toolkit. This has enabled a 5 hour reconstruction process to be completed in 15 minutes - a similar approach should be applicable to other areas of biomedical research.