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Learning to embrace the blips: the highs and lows of running workshops

By Linzy Elton, on 17 April 2023

My name is Linzy and for the last four and a half years I’ve been working as a postdoc researcher at the Centre for Clinical Microbiology at UCL in London. My job is pretty varied and I work on lots of different projects, including antimicrobial resistance, clinical microbiology, tuberculosis and sequencing methodology.

I’m also part of some large African-led research consortia, including PANDORA-ID-NET, which aims to provide a scientific response to emerging infectious diseases and the Central African Network for Tuberculosis, HIV/AIDs and Malaria. This means that I am also involved in a lot of training and capacity development projects, including providing DNA sequencing training for our African collaborators. DNA sequencing of pathogens such as Mycobacterium tuberculosis is an increasingly way that drug resistance is detected, and how outbreaks can be tracked.

I’ve just got back from running a TB DNA sequencing workshop with our collaborators HerpeZ in Lusaka, the capital of Zambia, and have been reflecting on the joys and difficulties of organizing these events.

The calm before the storm – Dr John Tembo and I getting the equipment and samples ready

It’s not the first workshop I’ve run, it’s not even the first workshop I’ve run on TB sequencing. This wasn’t my first rodeo. Yet it doesn’t seem to matter how many times you’ve done something, nothing can ever quite prepare you for setting up in a new lab for the first time, especially if that lab is in a different country.

This event was based on the use of a small device called a Nanopore MinION and the accompanying flow cell, into which you load your DNA, and which contains tiny pores through which the DNA molecules wriggle.  As they do that, small electrical changes occur related to the DNA sequence, and these are recorded and later decoded. The point is that the barrier for set up and infrastructure needed for this technology is low, so these can in principle allow DNA sequencing in parts of the world that would find it less easy to run some of the more high maintenance alternatives.

MinION device on its way to Zambia

The MinION device on its way to Lusaka

However, while I could take the MinION on the plane, delays at customs for our reagents meant we had to move the workshop back by four months. We also blew up the electrophoresis gel tank. Twice. The NanoDrop DNA quantifier we borrowed simply refused to comply with the software on our lab’s new sequencing computer. Pipette tips didn’t always fit the array of pipette brands that we had collected so that multiple groups could work at once. It was so forcefully air-conditioned in the lab, that the two MinIONs I had brought with me were unable to get to the necessary temperature without cocooning them in someone’s armpit (often the hottest countries seem to have the coldest labs). It took hours to discover that the internet, which John Tembo, Scientific Officer at HerpeZ, had bought at great expense (requested as a result of previous experience, more on which later) had firewalled three essential – and entirely benign – files in the data analysis software the participants needed to download. And Zoom failed to sensibly record most of the presentations, meaning I’ve spent hours trying to edit them for the Global Health Network website.

Preparing the DNA to load into the MinION device

Despite (or perhaps because of) these issues and those I have encountered before, the workshop was an overwhelming success. Each of the participants was able to quantify their DNA samples using the well-behaved Qubit machine (always worth having multiple options) and learned how to load practice flow cells (by the end of the day they were sick of me waffling on about air bubbles). Everyone was able to participate in the preparation of sequencing libraries (which are DNA samples that have been treated to make them flow through the pores), and each of our three sequencing runs worked beautifully.

Big, medium and small sequencing computer setups – the MinION device actually running the sample is sitting on the top of the computer tower

Even the day of bioinformatics (where the data outputs from the MinIONs are decoded and the DNA sequences analysed using computers), often a difficult one for traditionally lab-based scientists to get to grips with, went surprisingly smoothly. Having run a similar workshop at NIMR in Tanzania in August last year, I streamlined this workshop drastically. At NIMR, the internet was so weak that the participants weren’t able to download any software or test sequence files at all, so rather than being able to practice on their own machines, they had to make do with watching us demonstrate, which is not very inspiring. This time round, despite the internet playing hide and seek with some of the files, we managed to get pretty much everyone successfully base-calling the data (decoding the output into the DNA sequence), on both Mac and Windows laptops.

The slow internet had also been an issue previously when starting the sequencing runs: MinIONs need to connect to the Nanopore servers elsewhere in the world just to start up (after which they can disconnect), and in Tanzania, they just couldn’t connect. So there we had people trying to find WiFi and mobile hot spots, and IT people waving ethernet cables and WiFi dongles about. It was chaos, but after six attempts it started, to our immense collective relief. This time in Zambia, we started three sequencing runs simultaneously with no problems (apart from the aforementioned too-cold MinIONs).

Learning how to extract TB DNA

Problems are always going to arise when pulling together an event with different disciplines and multiple groups involved. At times it can be incredibly frustrating, and if it happens in front of the participants, it can feel embarrassing that it looks like you don’t know what you’re doing. Whilst it can be a little awkward, I’ve learned to embrace the blips. Indeed, I’ve learned an awful lot more about running workshops and the techniques I’ve been teaching when troubleshooting the things that go wrong. I’ve learned to incorporate that into the training itself too. Things won’t be perfect when the participants take this away into their own settings either; far from it, they’re likely to encounter all sorts of issues. Learning how to sort them out themselves might well be one of the most useful lessons they take away.

I’ve added all of this experience into our PANDORA Global Health Network hub tutorial pages. You can click on the links to learn more about sequencing generally (including laboratory set up, bioinformatics and video tutorials), and specifically about tuberculosis sequencing using the Oxford Nanopore approach.

Linzy Elton is a postdoctoral researcher at the Centre for Clinical Microbiology at UCL.

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