Travel story: Melanie Smith

Melanie Smith from the Robinson Research Institute travelled to Brisbane in July to attend the Winter School in Mathematical and Computational Biology.

This is what Melanie had to say about her experience.

What was a highlight of the travel?

The UofA is the only university I have any experience in. Spending time at another Australian University with incredible facilities was a highlight. Also, being immersed in computational biology and cutting-edge research in the format provided was amazing.

Did you attend any workshops, labs, research facilities or attend any meetings associated with your travel?

Yes, on Monday Dr Christopher Noune, a next-generation sequencing technical officer from AGRF, gave a short workshop. To date I only have experience with Illumina sequencing, so it was fascinating to learn about other technologies such as ThermoFisher, Roche (454), BGI and PACBIO (3rd Gen). The talk was particularly informative regarding the pros and cons of each technology as well as a number of methods to identify bias in sequencing technologies. There was also a very interesting impromptu panel discussion/satellite meeting on Wednesday which included topics such as Career Strategies, Women in STEM, and Science Communication. I was particularly interested in the topic of Women in STEM and found the conversation insightful. In particular – questions relating to increasing the number of women in STEM were always directed (or redirected by the chair) to the women panellists, as if the entire burden lay in their hands. There was also a discussion surrounding the requirement for free access to data, and compute resources that highlighted for me how open and well-resourced our candidature at the RRI is.

Did you visit any other labs or research facilities?

Yes, we visited Institute for Molecular Bioscience (IMB) in The University of Queensland on Wednesday. The IBM is focussed primarily on research in the genomics of development and disease, cell biology and molecular medicine, and chemistry and structural biology. As a bioinformatician it is always important to be aware of and have a working understanding of the various techniques used in the procurement of the data sets we work with. This understanding helps to identify the different biases and peculiarities of laboratory techniques and being reminded of this forced me to go back and ensure I understood the provenance of the data I see day to day.

Did you meet any researchers or collaborators of significance? Why are they important to your work?

I spoke on Monday with Dr Felicity Newell and Mr John Pearson from the QIMR Berghofer Medical Research Institute. Felicity gave me some great advice on the challenges of NGS mapping and alignment, in particular on the difficulties of placing short reads (my research is in small RNAs so this is relevant). We discussed alignment algorithms and the challenge of choosing an appropriate aligner. I was especially impressed with her pragmatic, solution-driven approach. John (as a technician) was very knowledgeable about “what can go wrong in the lab” and gave me some great advice about identifying sample quality, sample mix-ups, sample cellularity and ploidy, library quality (including fragment size selection) and library mix-ups, which I have subsequently identified in my own data. On Tuesday I spoke with Dr Joshua Ho from the Victor Chang Cardiac Research Institute. The lecture Joshua gave was not directly relevant to my work as he focussed on single cell sequencing, but I was curious to learn more about how he accounts for drop out data in his work. I am currently working to identify possible biomarkers of pregnancy health in maternal plasma and find the within group variance very high. My initial idea was to take his method for dealing with the lost data and apply it to my own work. After discussing (on my return) with my supervisor the method is not directly appropriate, but we are working on the development of a new method which may prove very useful.

How will the experience support you and your research going forward?

From the Winter School I know how other researchers analysing data using mathematical and computational methods and what is the proper way of doing research in bioinformatics.

What was the most exciting thing you learned/experienced whilst traveling?

The most exciting thing for me was to meet and talk with so many women with an interest in bioinformatics and computational biology. It has also inspired me to reach out to our local chapter of R-Ladies (literally women who use the R programming language). I didn’t realise that there are R-Ladies chapters all over the world with forums for everything from mentoring and programming and surviving as a mother in a STEM career. After reaching out I became aware that our local chapter has essentially closed as the women involved have moved interstate. Since then I have spoken with my primary supervisor and members of the Bioinformatics Hub who are keen to re-establish a R-Ladies presence in Adelaide. This to me is very exciting.

What was the most interesting or unexpected moment of your travel?

The 2018 Winter School provided an amazing line up of female lecturers. For me, this inclusion of women helped me see a future in STEM, and in research. The feeling of inclusion, and of belonging in the Bioinformatics community was the most unexpected experience.