The Elective Perspective | Jes | Part 1

Week 1

The Kinghorn Centre for Clinical Genomics, Sydney, Australia. This is where I’m lucky enough to be doing my elective placement for 6 weeks as part of the STP. The Kinghorn Centre for Clinical Genomics (KCCG) is part of the Garvan Institute, a prestigious medical research facility, and as the name suggests- specialises in Genomics diagnostics and research.

I am spending my time here working with a scientist named Andre, who works on the translational genome informatics team. This means the research this team does sits at the incredibly interesting and dynamic intersection of where research and diagnostics meet- not quite used diagnostically, but also not too far fetched from reality.

I thought about going into detail about the work I’m doing day-to-day, but that’s probably not going to be of interest to the majority of non-bioinformatician readers. So I’ll keep it brief on that part and focus mainly on the things I’m learning professionally and write candidly about the experience as a whole and I hope that’s something people are interested in reading!

My first week consisted of inductions and meeting everyone in my office. I spoke to my supervisor about how the work I could do over the next 6 weeks could fit into his project. His project, broadly speaking is looking at whole genome sequencing data from two pediatric cancer patients, sequenced using nanopore, and essentially just seeing what he can find, also comparing it to what was found using illumina sequencing. So my first week was a crash course introduction to nanopore bioinformatics pipelines and the HPC cluster and getting my head around it’s quirks and differences to what I am used to. By the end of the first week, it took a while to get there, but I submitted my first jobs to the queue to run over the weekend.

Week 2

Turns out I conveniently arranged my placement to include a NSW public holiday, which meant I could safely enjoy the National Rugby League final on Sunday evening from the pub without worrying about a hangover on Monday morning. So week 2 really started on Tuesday, which was fine by me! So that job I submitted to run over the weekend? Obviously it didn’t work. Turns out the process needs a lot more compute power than your average (supercomputer) CPU can provide. I needed to use the GPU instead. This isn’t something I know a lot about so it was interesting to have to figure out the nuances of running programs on a GPU as well as thinking more about time, memory and compute limitations, which is not something I’m used to doing in a diagnostic setting.

Tuesday and Wednesday my supervisor wasn’t in so I was left largely to my own devices. This was both good and challenging. While my supervisor was contactable by email and very responsive, I felt I couldn’t email about every challenge I faced where I may have just quickly nipped over to his desk and asked had he been in the office. While this pushed me a bit out of my comfort zone to not have the safety net of another pair of eyes, it encouraged me to use my problem solving skills and I think even just 2 days unsupervised immensely improved my confidence in navigating the computing cluster and understanding some of the new commands. Thursday was a pretty good day- and not just because I met my friend for lunch at a place that exclusively serves hummus and actively encourages the consumption of an entire bowl of it for lunch. But, also because I finally made a bit of progress running my commands. Friday I managed to re-submit the jobs and i’m crossing my fingers that I’ll come in on Monday morning to empty error logs and exactly the output I requested. We will see…

A reflection

How has it been 2 weeks already?! It’s honestly come around so quickly. I’m making slow progress and it’s good to be moving forward, but also discouraging at times as I wish things could go faster. But looking at everything I’ve learned already I’ve got to appreciate that I’m adapting to a whole different way of working and using new technologies and techniques that I’ve never used before, and go a little easier on myself.

Starting somewhere new and different is always a little bit overwhelming. I definitely came into the elective with a positive attitude but for some reason started off feeling out of my depth and almost like I’d made a bit of a mistake. I think starting off a research project there’s always a little bit uncertainty about where it’s going to go and the scope can be quite vague. I think I’d put a lot of pressure on myself to understand too much about the direction of the project too quickly, as I knew I only had 6 weeks to really get as much out of this experience as possible.

However, having said that, by the end of my first week I was feeling alot happier and grateful about my situation. Looking back, it’s obvious it was just a combination of first day nerves, jet lag and overthinking things- the same way I do when anything new happens. But it really didn’t take long for excitement about what’s to come with this project to take over, even though I’m still not entirely sure what that may be. In just two weeks I’ve been exposed to so much interesting research that’s going on so I’m excited for what I can learn in six!

Other than work, my first weeks found me sampling as many Australian eateries, pubs and vineyards as is physically possible (and healthy) to do within 14 days, and exploring the city and nearby areas by land (Blue Mountains hike) and sea (Ferry across the Harbour).

It is unfortunately set to be raining this weekend (I know right?!) so I have no choice but to explore Sydney from inside- pubs, cafes, restaurants and maybe a museum or art gallery too- if there’s time. But on a serious note we are actually planning on checking out the famous Glebe markets on Saturday and if it’s not tipping it down, go for a coastal walk from Watsons bay to Circular Quay on Sunday.

I’m very appreciative of the opportunity to be here and have already learned so much. I’m looking forward to see what the next 4 weeks will bring. I hope you enjoyed reading this and come back to read more in a couple of weeks time!

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