Week 3
When I say that coming in on Monday morning to find that all 12 of the jobs I left running over the weekend had executed perfectly brought equal amounts of surprise, joy and relief, you may think “you should have more confidence in your abilities”. But I think most bioinformaticians will know the suspense of checking the log files for a job that has been running for 20+ hours and not wanting to get our hopes up too high- just in case. But of course, there was no time to linger on that success as it was only the first stage of a multistep pipeline.
This week I was lucky enough to attend a two-day “Introduction to Nanopore” workshop run by Oxford Nanopore, including the wet lab protocol on day 1 and data analysis on day 2. This was such an informative two days and I even got to load my own flow cell with cane toad DNA (the lab who provided the DNA are planning on using long-read sequencing to improve the reference genome of the cane toad with the intention of enabling them to develop specific biocontrols for this invasive species in Australia). The flow cells can be totally ruined if you get an air bubble in them, so, let me tell you- after not having touched a pipette in about 4 years this was a pretty tense experience. We also ran through a lot of the bioinformatics tools available for processing the data and what struck me was how many were community-developed tools; Nanopore has a very active online community that is great for developing and troubleshooting.
Thursday I was introduced to afternoon tea, which is not dissimilar but not identical to afternoon tea in England. Apparently, every other week employees across several floors come to one of the meeting rooms to chat and eat cake for about 15 minutes. I think this is a really nice way for people who wouldn’t normally see each other very often at work to socialise a bit and make everyone feel like a team. Perhaps something we could introduce in Exeter…?
A full 5 days at work after a 4 day week is always tough, but I managed to sail through Friday without any major hiccups into the weekend- which, sticking with the theme, involved food, wine and beaches!
Week 4
The weekend full of sun, sand and sea passed far too quickly and Monday morning meant I was kept inside away from the glorious sun for another 5 days. This week mainly involved plugging away my project. What I really mean by “plugging away” is that I ran into a lot of brick walls installing software and battling with GPU configurations. It was frustrating at times, but it made me realise that a lot of what we do (and this is probably transferable across specialisms) isn’t about knowing all the answers, or knowing exactly how to do something, but about being able to apply our knowledge, use problem solving skills to find novel solutions and learn from the people around us. Something we don’t get to do in diagnostics very often, is sit at our computers and chip away at a problem until we find the solution- we don’t have time for it. This is one of the biggest limitations of working in diagnostics- it’s difficult to implement new processes quickly, even if they’re more efficient because the demand of urgent diagnostic work is unrelenting. Don’t get me wrong, providing diagnoses is the most rewarding part of the job, but being in a research setting has made me appreciate getting the time to work on something without thinking about the one hundred other things I need to be doing (trying not to think about my MSc project or competencies right now…)!
Friday afternoon brought about the success of getting a program to run that – I wish I was lying – I’d been battling with for the entire week. Always a nice way to end the week and also hopefully lead to a good start on Monday morning!
On Friday I also organised to have a conversation with Mary-Anne, a genetic counsellor and co-director of KCCG to talk about the diagnostics side of the services they provide. I felt like it was important to understand how the patient pathway and services available clinically differ from England. I was pleasantly surprised to find that in general it’s not so different. There is a 2-tier health system in Australia, public and private sector. Genetic testing is offered in the public sector and patients can be referred to genetic counsellors and clinical geneticists for assessment on whether they are suitable for a genetic test. The process is much the same State to State but my understanding is that sequencing is done by laboratories within the State rather than being centralised, as we are moving towards in the UK for WGS. They also have the Australian Genomics Health Alliance research study which draws parallels to the 100K Genomes Project in the UK. The Garvan is primarily a research institute but they also offer a NATA accredited diagnostic sequencing service for Whole Genomes and to a lesser extent Whole Exomes. They are a data-only service meaning they don’t do any clinical interpretation here and only do primary bioinformatics- the data is returned to the referrer for interpretation. I am hoping to have a tour of their sequencing labs next week and talk to the service bioinformaticians to find out exactly what their pipeline does.
It was also unfortunate to observe that Australia faces the same struggles as England in certain aspects- particularly, direct to consumer testing (although they have published a handy guide for consumers) and a shortage of key genomics professionals such as genomic counsellors. It was a really interesting glance into Genomics in Australia and the clinical service at the Garvan and I’m looking forward to talking to some more people next week to get a further understanding.
Reflection
⅔ done. I’m having a really great time and learning so much- it’s difficult to comprehend just how much I’ve actually experienced in the past 2 weeks. But contradictory to that I also haven’t made as much progress with my project as I was hoping to, and with only 2 weeks left there’s only so much I can fit in and I don’t want to look back and think “I could’ve got more out of that experience”. Having said that I’m trying to look at the elective as a fun experience as well as educational, and not stress myself out by running myself into the ground by trying to do everything.
I’ve not got much more to add on the reflection side of things- short and sweet. I hope people are still enjoying the read and it’s not too bioinformatics heavy! My plan is to post another update after my final 2 weeks of my elective and then you never have to hear about it again (unless we meet in person and then I probably won’t stop talking about the 6 weeks I spent in Sydney for at least a year). Until next time!
STP Perspectives 