I'm a data engineer with a background in bioinformatics. I currently work for the Next-Generation Precision Medicine Program (NGPMP) at the Hudson Institute's Centre for Cancer Research (CCR).
Our program produces terabytes of data that has to be stored, processed, cleaned, and annotated before being disseminated to researchers for downstream analysis. My role as data engineer is to effectively manage the above data lifecycle so that researchers can spend more time on analysis and less time on data wrangling.
This was a challenge when I first started the role, as no data strategy or
governance plan was in place, so it was my responsibility to draft and implement
such plans. The approach I chose for our small team of three was to leverage
existing open-source genomics pipelines (e.g. nf-core community
pipelines) where possible, minimising the overhead
maintenance and development associated with in-house pipelines. Costs are
further reduced by using freely available resources such as MASSIVE
M3 as our cluster environment and the ARDC
Nectar Research Cloud
as our database host. Across our codebases, I also try to restrict the number of
frameworks and languages used to common competencies in the fields of biology
and bioinformatics (E.g. Bash, R, Python, SQL) to minimise the cost associated
with training.
I am well versed in bioinformatics, which is a requirement in order to effectively and accurately process a broad variety of genomic data. Apart from my love of data engineering, I am also passionate about using statistics and effective data visualisation to make data-driven decisions. My other hobbies include:
- 🪓 Woodworking (i.e. collecting tools that I may someday use)
- 🕹️ Gaming (the more byzantine, the better e.g. Dwarf Fortress, Underrail)
- 📷 Photography (I was particularly prolific when I studied agriculture, and there were plenty of canola fields...)
I am happy to connect with new people in the field of bioinformatics, data engineering, and research support in general, so feel free to send me a message on LinkedIn!
