As a software engineer I provide a breadth of computing knowledge and software development expertise to many of the projects within the group. This can vary from providing advice about best practice for data transfers and processing to developing the hardware, administrative tools and user interfaces to manage new sequencing technologies.
What are your main projects currently?
A lot of my work currently revolves around integrating Nanopore sequencing into the groups workflows and reinventing how to run pipelines that produce data such as species and related samples. The common thread with these projects are allowing the group to move from sequencing hundreds of samples every year to thousands whilst minimizing the amount of “wasted” resources that don’t scale effectively. We are achieving this by using a variety of computing resources such as in-house servers with Graphic Processing Units (GPUs), High Performance Computing (HPC) clusters and cloud environment (e.g. Microsoft Azure, Amazon AWS).
How I got into this position
I started my undergraduate degree in Computing at Leeds and took many of the Computer Graphics modules available during the course as well as a project on how GPUs can accelerate some forms of processing. This lead my future PhD supervisor to tempt me with working on a wall-sized display made up of 24 monitors and thus I committed to a further 4 years of study! My PhD improved many of my analytical skills to quickly understand and question the core elements of a problem as well as making me try many different software libraries and packages, skills which are of vital importance in my current job!
My interest in working in a medical environment began when taking a short-term position with colleagues of the department, during which I was tasked with implementing new functionality for aligning a 3D pathological model of the throat with an MRI volume of the patient. This lead to a further post in Linköping, Sweden, where my office was about 10 meters away from an MRI machine! Encountering these sorts of scenarios and as well as the close collaborations you get to have with a variety of different people doing this interesting and varied work is one the reasons I enjoy my work here so much. Well that and the cake every week…