School of Infection & Immunity

Participants from around the world last week 'attended' the third annual Glasgow Bioinformatics Summer School led by Dr Thomas Otto and Dr Kathryn Crouch.

The week-long course provides experimental biologists working with omics data with a comprehension of bioinformatics language and terminology, an understanding of the underlying concepts, and experience in genomic-scale data analysis.

Although the COVID-19 pandemic meant the workshop could not be run in person this year and was instead delivered virtually, it also meant the number of participants was unrestricted by room capacity.

Dr Otto and Dr Crouch were, therefore, able to welcome 57 participants, of which around half were from the University of Glasgow while a few worked across time zones from the US and Japan.

Material covered ranged from the basics of using Linux and R on a remote server through whole genome sequencing analysis, bulk RNA sequencing analysis, single cell RNA sequencing analysis and functional enrichment methods.

Zoom was used as the primary interface, with lectures delivered to the whole group while breakout rooms of five to seven participants were utilised for smaller discussion sessions and practical exercises, with instructors moving between them as required.

MS Teams was used as a supplementary method for sharing information. Participants were provided with a downloadable virtual Linux computer with software and data pre-installed for the majority of the exercises, supplemented with access to a larger server for more complex analysis and use of online platforms such as Jupyter notebooks.

Facilitating participant networking virtually was one of the harder aspects to manage but the instructors endeavoured to mix up the breakout rooms by asking participants to add thematic information (hobby, pet, etc) to their Zoom username and assigning participants to rooms accordingly. They also had some fun with slide-deck bingo and other fun games.

As always, the highlight was the group project, where groups complete a half-day self-guided analysis project of their choice and present the results.

Dr Otto said: "It is always great to see how people are able to apply the learning objectives to a project of their own.

"This year, single-cell RNA-Seq analysis was dominant and all the presentations were of a high standard.

"While the first time running a virtual workshop is never going to be as slick as one would like, the response from students on Twitter and the preliminary feedback from the course evaluation was overwhelmingly positive.

"We can look back on a successful workshop, while of course taking away some learning outcomes of our own.

"If you want to get in on the bioinformatics action, we anticipate opening applications for next year's summer school in February."

Dr Crouch added: "We would like to thank the students and staff who gave up their time to make this happen.

"We couldn't manage without our co-instructors and their outstanding enthusiasm, so many thanks to Ross Laidlaw, Patrick Shearer, Alex Pancheva, Domenico Somma, Roan Zaied, Lucy MacDonald and Emma Briggs. 

"Our sincere and grateful thanks also go to Scott Arkison for setting up and maintaining all the computational resources, and Regina Marti-Schindler for keeping track of all the students."

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First published: 7 September 2020