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Focus on the Course Context
Identifying the target audience is important for achieving the learning outcomes. Dr Ben Moore explains his experience of creating tailored content.
[THEME SONG] Hi my name is Alice Matimba from Wellcome Connecting Science. I developed and organise Genomics and Bioinformatics training. Joining me is Ben Moore and he is the Outreach Manager, for the Ensembl Genome Browser . Today we’re going to talk about the course that he delivered in Romania in 2020. Welcome Ben. Thank you Alice. So as part of the Ensembl Genome training programme, you delivered a half day workshop in November 2020, which was part of the Romanian Society of Bioinformatics course on the study of Antimicrobial Resistance using Genomics. Could you give us more details on what the course was about, and who was the target audience.
The Ensembl Outreach Team, usually delivers workshops for scientists all around the world who are interested in using the Ensembl Genome Browser to retrieve data that might be able to help them, in their areas of research and we deliver courses to a wide range of different types of scientists who are studying a wide array of different topics. So the Romanian Society of Bioinformatics contacted us early in 2020. And they hoped that we’ll be able to contribute to a two day course that they were running, that was focused on Antimicrobial Resistance. So they had a group of around 30 to 40 junior and senior researchers, that were all working on the area of Antimicrobial resistance.
And they wanted us to deliver a half day, hands on practical workshop, and teaching the trainees about the different data that we had in the Ensembl Genome Browser and the tools that are available, that might be able to help them in that work. And how did you tailor you’re teaching materials for this course, and what type of resources did you use ? So usually in the Ensembl Browser workshops we use human, the human genome assembly and annotation as the example species.
This is because human has one of the highest quality genome assemblies of all the species that have had their genome sequenced, and the annotation and the available data sets are also very high quality and– then there are lots of different available data sets that people can explore, and look into during the workshops. However, obviously we were thinking about an audience that were very particularly interested in studying antimicrobial resistance. So what we needed to do for this workshop was to create some tailored course materials, that focused on bacteria and then in particular antimicrobial resistance.
So what I decided to do was to develop a course using the Ensembl Genomes, Genome Browser, which is a sister project that we have that presents gene, a genome assembly and annotation data for non-vertebrate species, including bacteria. So I decided to start off with an introductory module, because not all of the audience– not all of the trainees that would be in the workshop would have used Ensembl before. We started with an introductory module, that covered the sources of the data that we have in the Ensembl Genome Browser, and the backgrounds where that data comes from and how it’s processed and presented in the browser itself.
So, what we did was we focused on the bacterial genomes, and the gene the bacterial genome annotation. Thinking about how Ensembl imports that data into the Genome Browser, and then specifically how some of the annotation is then linked to antimicrobial resistance. And that gave them an opportunity to begin thinking about how the browser works in the context specifically of bacteria and antimicrobial resistance. I then moved on, in the second part of the module two presenting the Ensembl Variant Effect Predictor. That’s a tool that we have in the Ensembl Browser that is useful for people who want to predict the molecular consequences of genomic variants.
So if a scientist has performed some of their own sequencing experiments and they have a variation data set, and they want to investigate that data set in more detail, to prioritise variants, think about the molecular consequences of those variants. Then the Ensembl Variant Effect Predictor Tool, can help annotate those variants providing output for the scientists to continue their evaluation of the variants that they’ve identified. The great thing about the Ensembl Variant Effect Predictor is that you can actually use it with any species. So as long as you have a genome assembly and annotation and annotation sets, you can use the Variant Effect Predictor Tool in your variant analysis.
So what I did was, I used example data sets that were lifted from publications that have studied antimicrobial resistance. So they were two that I found that were very interesting. There was a case of, of antimicrobial resistance strain MRSA, that was found in a Neonatal Hospital in Addenbrooke’s Hospital in Cambridge here in the UK. So I took an example data set from that study, and I also looked at a study of multidrug resistant tuberculosis that was identified in a clinic in Uganda. So I used two example data sets from pre-existing publications.
And used those in the hands on demos and exercises, just to really allow the students to explore the data and the tools in the context of the area of their research. So the whole aim of that was to present the data and tools available in Ensembl. In a context that the audience could relate to and apply to their own practice. OK so I understand that this course was originally intended to be run as a face to face event, but was switched to a virtual learning environment due to the COVID-19 pandemic. So how did you adapt your teaching approach style to deliver the workshop ?
So the Romanian Society of Bioinformatics, they contacted us early in 2020 which meant that originally the course was being organised as a face to face course, before the restrictions of the coronavirus pandemic came into force around the world. So it was only after the course had already been partly organised that we had to switch to a virtual format, and it was shifted to later in 2020.
Obviously, one of the challenges would be that this course would be delivered virtually, so what we had to do is think about how we could make sure that the learning environment was still effective, in being able to reach the learning objectives and allow the trainees the hands on experience of using the Ensembl Genome Browser to, explore these data sets and use the tools that they would hopefully then use later on in their work. So there were a number of ways that we did this, so we used the Zoom platform. Which I think is very common among scientific training and also many other aspects of our life now, and we used Zoom.
So within Zoom there obviously a number of ways that you can maintain interaction with users. So we obviously used the chat box and we also used the Zoom reactions. The Zoom reactions allowed me to see how the students were keeping up with the course and to provide instantaneous feedback of how they were finding the different modules and the exercises. So it meant that I could keep an appropriate pace of teaching in the course, not going too fast or too slow if people were either struggling to keep up for example.
What we also did was we created a living doc, which is a solution that we’ve actually implemented in a lot of other courses that we’ve been running as well, which is a really great solution and facilitates– facilitates interaction between the trainees, between each of themselves and also with the trainer. So what we did, is we created a blank Google document. And gave everyone on the course rights read and write access to the document. And encourage them to put notes, and then also to ask questions on the document itself. And then the trainer could obviously visit, the living doc throughout the course. And answer the questions extensively with screenshots with links to other documentation other references as well.
And then obviously, that document grew and grew over the course and then eventually became a really nice knowledge base that the students could take away, after the course and continue to use as a reference if they wanted to as well. Well thank you very much Ben. That was very insightful, and it seems you had a very successful virtual workshop. Thank you for your time goodbye Thanks Alice goodbye.
Identifying the target audience is important for determining the learning outcomes. Dr Ben Moore explains his experience of creating tailored content.
He also explains why he chose to include in his course the Ensembl Variant Effect Predictor, a tool that can be used with any species, including bacteria, and is really useful for scientists who have performed their own sequencing and have their own variation datasets.
For the exercises associated with the Variant Effect Predictor, Dr Ben Moore used small datasets lifted from publications that studied anti-microbial resistance in different contexts – one in a maternity unit in a hospital in Cambridge, UK, another from a study that focussed on multidrug resistant TB in a health centre in Uganda.
We also learn how Dr Ben Moore adapted the workshop for a virtual learning environment due to the COVID-19 pandemic. We learn how Ben used the features of the Zoom platform, including live-polling, to increase audience interaction and gauge students’ progress against the learning objectives. Ben also used a Google ‘Living Doc’ as a platform for students to collaboratively make notes and ask questions. The Living Doc was a really useful tool to promote interaction and the final product served as a useful knowledge-bank for all of the students to use as a reference.
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Train the Trainer: Design Genomics and Bioinformatics Training
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Train the Trainer: Design Genomics and Bioinformatics Training
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