Improving Our Internal Workflow with Automation

José Maria “Txema” Rincon Garriz

I have always been drawn to science, any kind of science. I chose to pursue studies in biology in Geneva. 20 years ago, I obtained my Master’s degree in Microbiology based in molecular biology. My first research work at the time was on understanding the remodeling of structural proteins involved in the apical growth (tubulin mainly) of Neurospora Crassa filamentous funghi. That’s how I discovered molecular biology and got first acquainted with the field of genomics.

I was not willing to follow a typical path though, and got tempted to explore different scientific horizons: first, I decided to further my education with a PhD and moved to a laboratory involved in the control by transcription factors of the acute phase of the steroidogenesis in the adrenal gland. We focused our research in the rate-limiting step of the process which is the transfer of cholesterol (the precursor of all steroids) into the mitochondria to be converted into a steroid.

Then, after my PhD, I took another turn again with a postdoctoral researcher position in the field of immunology of transplantation. The research work was based on controlling the Graft Versus Host Disease (GVHD) after a bone marrow transplantation.

After 2.5 years, I left the academic world and tried my luck in the industry. I started working in R&D for a company active in NGS and that’s when I started to realize the potential of molecular biology and how it could improve diagnostics – and how fun working in that field was!

My job began to revolve around automated systems, and I started to understand the power they had by reducing costs and time. Although testing scripts on automated systems takes time and needs long-term visualization and a lot of concentration, the task seemed to me an enjoyable one. I’ve played chess for more than 30 years, and we all know that chess is all about visualization and concentration. I love spending time analyzing a problem, thinking it through and assessing how we can improve or speed up processes even though they are already working properly. Optimizing resources has always been a challenge I liked to take, and I think I developed this skill while playing board games.

I first heard about SOPHiA GENETICS after 2 years spent in that company. They seemed like a promising start-up, a pioneer in the analysis of NGS data, and I knew I needed to become part of their journey. In 2016, I quit my job and joined SOPHiA GENETICS. It’s been 5 years now since I started working in our Genomics Laboratory in Geneva, and I had the opportunity to wear many hats already: I did some R&D and provided demos for customers, to help them improve their skills and enter easily into routine.

We quickly acquired our 1st automated systems though, and we immediately started to implement and validate our workflows on these new tools. Now, I am in charge of the automation of our solutions in the lab. I typically spend time implementing scripts, testing them and training my colleagues to use our automation instruments

to improve our internal workflow. My job is very rewarding in the sense that I can directly see its value for the company: it has already allowed us to speed up treatment of Biopharma and SOPHiA Integrated Solution research projects but also to perform quality checks in the lab. I am really proud to have contributed to these through my implementing and/or validating of several scripts.

It is both exciting and challenging for me to be working on new solutions and improving our established workflow, but the environment also plays a great deal in my love for the job. To be around positive and committed people is a great feeling; the company’s mission gives us all purpose, and it’s not something you can find in a lot of places. My hope for the future is that we keep thriving and face all the next hurdles and challenges that may arise, only to become greater and better, while maintaining this mindset that makes the SOPHiA GENETICS team truly unique, and the company a great place of work.