Postdoctoral Research Associate, Rosalind Franklin Institute

James Parkhurst is a postdoctoral research associate at the Rosalind Franklin Institute and Diamond Light Source, as well as an Academic Visitor at the University of Oxford.

Whilst obtaining his PhD, James worked at Diamond as a scientific programmer. His work on the Diffraction Integration for Advanced Light Sources (DIALS) project has had a significant impact for structural biologists working at Diamond and around the world. DIALS is used to automatically process every MX dataset collected at Diamond and other synchrotrons and has been used in the determination of thousands of protein structures.

James is currently developing an independent research programme using simulation and modelling approaches for the specification of Transmission Electron Microscope (TEM) hardware and system requirements, offline optimisation of data acquisition parameters and determination of data collection strategies for cryo-ET. He also develops novel software for solving challenging data analysis and reconstruction problems for in-situ cryo-ET. As part of this work, he developed the Parakeet TEM Digital Twin package.

He has already collaborated closely with researchers and software developers within Scientific Computing, including CCP4 and CCPEM. James is working on implementing software for the alignment and reconstruction of cryo-ET data from pillar shaped samples of biological specimens which may have general orientations not currently catered for by existing software. To achieve the best computational performance, an important part of this development is the use of GPU accelerators which also form a key aspect of upcoming DRI investments in the UK.

“CoSeC’s aims of supporting the advancement of computational research by developing and strengthening software to analyse and solve increasingly complex problems in multiple disciplines match well with the priorities and objectives of my research,” explains James. “The goals of CoSeC align well with my own professional goals and my work has already been fully embedded in the research software ecosystem of STFC for many years.”