The Digest

Connor grew up in Brisbane, Australia, and got an undergraduate degree in Microbial Biotechnology at the University of Queensland. During his Ph.D. at the Australian Center for Ecogenomics, he transitioned to bioinformatics while analyzing metagenomic datasets from wastewater treatment plants. He furthered these skills during his postdoc at Caltech where he lead Bioinformatics efforts analyzing metagenomic, metaproteomic, and metatranscriptomic datasets of deep-sea microbial communities. He then did a short stint at Second Genome, working on developing and automating scientific pipelines using cloud computing. 

Connor chose to transition from environmental microbiology to working on the human microbiome because he wanted to have a greater and more direct impact on the general public than what he could achieve in academia.


Tell us a little bit about yourself, what does a data engineer do?

Ha, lots of things, the role varies from company to company so I’ll tell you what a data engineer does at Pendulum. I build tools/programs/applications for the scientists in our R&D and manufacturing teams to help them do their jobs. But a lot of those tools are specifically about taking the raw data that we get from the various pieces of equipment and converting it into something that is more manageable to look at and work within the company. We produce lots of data to the point that you can’t just open it up in excel and play with it. A lot of my job is running programs that make summaries of the raw data so that other people in the company can get answers sooner.

What experiences shaped who you are?

I think my Ph.D. was pretty influential. It changed my career trajectory pretty drastically as it was when I was first introduced to programming. Before that, I was trained in microbiology and spent all my time in the lab, but during my Ph.D., I got introduced to bioinformatics and really loved being able to get a computer to do all my work. That had a flow-on effect that got me a job at Caltech, which sponsored a work visa in America and gave me the opportunity to live and work here. And of course, without that, I wouldn’t be at Pendulum right now.

What was it that made you want to join Pendulum?

I have a pretty diverse skill set that lets me work on software but still have a very good understanding of microbiology. When I decided to leave academia I wanted to still make use of all this knowledge, which made the biotechnology industry pretty attractive as a career path and in particular companies working on the microbiome. I also really wanted to be at a place that had a clear path and product. It’s hard to be motivated when you’re not sure if what you’re doing has any impact, so I really liked that Pendulum was customer-focused and there was an actual real product that we were selling

You authored a blog post that was featured on Amazon Web Services (AWS) database. Briefly, can you tell us what this was about? 

Most of what I do at Pendulum is to build software for our scientists that let them understand our strains better. One of these pieces of software I wrote was a program that lets users explore all of the genes in our strains. Now, the blog post was a bit more specific as it focused on only a part of the program that stores all of the data in a service that AWS provides called Amazon Neptune. Neptune is a graph database that lets you store a collection of things that have relationships to other things. You can think of it like how websites work, there is a page (that’s the thing) that has links to lots of other pages (those are the relationships). The graph database is designed to make it really easy to find things based on their relationships and it turns out this is really good for biological data as there are so many relationships between genes, genomes, and all of the scientific research that has been built up over the years.

What is the significance behind being featured on a platform like AWS?

It’s great for the company to show off the technology that we’re using. It’s nice when a big company like AWS wants to share what we’re doing because they think it’s cool. It’s also nice for me personally to get some external recognition for the tools I’m working on.

This past year has certainly been one for the books. How have you managed the work-from-home life?

I definitely miss going into the office and jiving with everyone but I’ve been able to adapt pretty well. I’ve been lucky in that I rent a fairly spacious apartment with a spare bedroom, which has since become my home office. I swapped my train commute with afternoon walks to get out of the house and cultivated a growing menagerie of succulents.

What is the best part of your day, the time that matters the most to you?

For me, it’s the evening. I get to put down the computer and relax on the couch or watch the sunset from my balcony.