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Meet our team! WestGrid Support Staff: Gemma Hoad

Gemma Hoad joined WestGrid and the Research Computing Team at Simon Fraser University in 2018. Gemma has 20 years experience working in the bioinformatics sector of the biotechnology industry.

Her extensive experience covers data management of large medical and biological data sets, designing and writing reusable code, teaching coding techniques to manage shared data, managing web applications and identifying tasks which can be carried out by software rather than manually. Gemma has also worked for the Fiona Brinkman Laboratory at SFU and the Genome Sciences Centre (part of the BC Cancer Agency) in Vancouver as a Computational Biologist in management of next generation sequencing data.

Gemma has a MSc in Bioinformatics and a BSc in Biochemistry from the University of Manchester (United Kingdom). Her specialties include: Database (PostgreSQL, Oracle, MySQL), UNIX/Linux, Python, PERL, shell scripting workflows, product support, SVN, Git, and SGE.

How did you get involved with research computing?

It has been a long interesting path that lead me to join research computing so I shall try and keep it brief!

I grew up in the UK and completed a bachelor’s degree in biochemistry at the University of Manchester, with a year working at Glaxo SmithKline in a protein chemistry lab, conducting various assays and protein separation techniques. In my final year of university, I was unsure about what I wanted to do next but had heard good things about a new masters-level bioinformatics program at the university. Bioinformatics was in its infancy back then in 1997 and was taught at very few universities. But the choice to join this program proved to be a good one. Biology research was increasingly employing computational techniques to manage larger and larger datasets and the industry needed people who understood both the data and the IT skills to manage it.

I started out working in biotech startup companies in Cambridge, UK and subsequently the European Bioinformatics Institute, as a database and application developer, building and supporting systems to help biology researchers search, edit and analyze their data.

In 2010, my husband, son, and I moved to Canada. I had wanted to move to here since a trip to Ontario when I was 20 when I experienced what a beautiful country Canada was. However the ski hills around Vancouver won the vote on where to live! To start, I worked at the Genome Sciences Centre, building pipelines for next generation sequencing data and following this I moved to Fiona Brinkman’s microbiology and bioinformatics lab at Simon Fraser University. This is where I started interacting with the Research Computing Group while reworking the Brinkman Lab’s applications and IT platforms.

I was able to transfer into the Research Computing Group last summer and have continued to develop a more up-to-date backend to the Brinkman lab IT architecture with the fantastic help and support of my team members.

What does your current role with SFU / WestGrid / Compute Canada involve?

Currently I primarily support the Brinkman Lab - the lab members and their IT needs. I have experience with their web applications such as IslandViewer for predicting genomic islands and PsortB for predicting protein sub-cellular localization and I am moving these applications to newer platforms, modernizing the software and structure along the way.

As a member of Compute Canada’s National Bioinformatics Team I also help support biology researchers in building systems to allow them to analyze their data. The Bioinformatics National Team is a team of bioinformatics experts working in universities across Canada as part of the Compute Canada Federation. This team, lead by fellow WestGrid support staff Jamie Rosner at the University of British Columbia, is available to help answer bioinformatics questions by email and a web forum hosted at https://bioinformatics.computecanada.ca

Recently I was able to support WestGrid and the Bioinformatics Team at the Omics Research Day at Simon Fraser University, fielding questions from researchers about HPC and the resources available to them.

What were your takeaways as a representative of WestGrid from the 2019 Research Day presented by the Omics @SFU event?

The researchers I met at the event were primarily graduate students owing to the nature of the event, and had either very tightly defined computational needs (such as how to make the most out of GPU nodes for machine learning analyses) or were asking how to get started with WestGrid / Compute Canada.

The most common advice we gave was to write to support@westgrid.ca or support@computecanada.ca with any questions that arose in their work. The support team can either help by email or put you in touch with a local WestGrid team member who can meet with you.

Also, to come out of the day, it has become apparent people are not necessarily using the national platform’s resources in an efficient manner which can impact other users. The WestGrid team could find ways to identify this and advise researchers how to configure their scripts better.

Owing to most researchers at the event working in biology, we also took the opportunity to tell people about the Bioinformatics National Team and the services offered by that group in particular.

Any advice or tips to offer researchers to help them better use research computing resources?

The key is don’t be afraid to come and ask!

I encourage researchers to ask questions - any question. People are often reluctant to come forward or seek help. There are WestGrid / Compute Canada people on campuses across Canada who can sit with a researcher to show them the ropes and also people who can answer questions by email.