We bring together all things related to scientific training
Author: meredith
Meredith joined the training team in April 2019 as an Events Organiser, managing the logistics for a variety of onsite training courses, workshops and international training courses.
Jonathan is a Bioinformatician in the Gene Expression group. His role is to expand capacity for single-cell RNA-seq analysis, the Expression Atlas resource, in dialogue with the Human Cell Atlas project. Jon gives us his tips for when looking for scientific training and some inside information on what he would be if he wasn’t a Bioinformatician.
What is your research focus and why did you choose to become a scientist?
My answer here is going to be awkward, in that I don’t have a research focus! Much of my career has been as a ‘service’ Bioinformatician working in various bioscience institutes performing custom analysis for a variety of different experiment types in different biological fields. In my current role at EMBL-EBI I build and maintain RNA-seq pipelines we run the same way over a large number of experiments. In both cases, I use the outputs of other people’s research (tools as well as data) to produce the best results I can for the questions at hand.
I actually started out in Biochemistry due to a fascination with the molecular machinery of life. But I discovered early on that the lab was not for me, and I’ve been on the ‘dry’ side of things ever since.
Where do you see this field heading in the future?
In common with many other fields, machine learning and artificial intelligence will play progressively bigger roles in this field in the coming years, with ‘Big Tech’ companies such as Google having ever greater involvement. I’m sure this will be a double-edged sword, and people such as myself will have to run to keep up, but there’s no denying the potential of these techniques and I foresee some exciting results.
How has training influenced your career?
I’d say my early Bioinformatics training (a Masters by Research and PhD after that) was pretty pivotal for me, setting me on a whole new path. After that my training was more incremental, for example, some introductory RNA-seq analysis similar to that offered at EMBL-EBI, followed up with a lot of self-teaching.
What is your number one tip for people looking for scientific training?
Be focused, choose courses that are related to your immediate objectives, and have clear goals about what you want to get out of the training. If you don’t have ways to immediately apply and expand what you’ve learned then the training quickly fades. I often find it more useful to do training only once I’ve tried to do something myself, so that I know which bits are tricky for me and what questions I need to get answers for.
If you weren’t a scientist, what would you be?
I’d really love to study historical linguistics, an interest I’ve picked a bit late in the day. I also learned to dance a bit over the last several years, maybe I’m a professional dancer in another universe where I started earlier!
We virtually sat down with Varsha and quizzed her on where she thinks the field of Metagenomics is heading in the future; and some inside information on what you can expect from the course.
What is your research focus and why did you choose to become a scientist?
Using metagenomics to characterise the chicken and salmon gut microbiome and its functions.
I enjoyed learning about bacteria and how they thrived in various environments. This opened a world of different microbes from symbiotic, commensal to pathogenic and highly resistant. It was exciting! When working in a lab, we would receive pre-analysed sequencing data from bioinformaticians. My mentors at the time were supportive to indulge my curiosity as to how the analysis was performed and hence I chose to study bioinformatics. At EMBL-EBI I have the opportunity to learn about new tools and analysis methods frequently.
Where do you see this field heading in the future?
The continued expansion of novel genomes and annotations deposited in public archives will give us more and deeper insight into some elusive environments. Additionally, as statistical modelling becomes more popular, many of the methods we use for annotation are adopting machine learning techniques. The challenges will be the integration of different data types, judging the optimal cutoffs for accurate annotation, and continuing to ensure that all of these new types are easily available through community-adopted public repositories.
How has training influenced your career?
I have been lucky to have opportunities to attend training courses which helped tremendously with understanding the basics of a new subject. Also, a field such as metagenomics is progressing so fast that training gives a great snapshot of the recent updates and methods that others are using for similar research.
What is your number one tip for people looking for scientific training?
Keep up to date with upcoming courses which are interesting to you. Twitter or LinkedIn can be useful for this, or even the webpages of some of your favourite institutions. However, I found that asking colleagues and peers about training courses they have attended is most informative.
If you weren’t a scientist, what would you be?
To be honest, I went home one day from school and startled my parents with the news that bacteria are the new “cool” – so I’m not sure that I would have done something else! I enjoy singing and it might have been fun and challenging to pursue that.
Which methods and new technologies will be addressed in the course?
There is currently a lot of interest in generating metagenome assembled genomes (MAGs) from microbiome data, so we will work through this process including potential tools you might use for the various steps, as well as things to consider in controlling the quality of your data. An introduction to MGnify will also highlight the specialised pipelines used to analyse different types of microbiome data: amplicon, WGS reads, and assemblies.
What are the highlights of the course?
The course will give an overview of metagenomic data analysis including, browsing public data, quality control, and assembly of sequenced metagenomes, tools, and methods to analyse metagenomic data and submission to public archives. There will be a mixture of live and recorded talks, practicals, and Q&A’s with lots of opportunities for discussion. A personal highlight is the chance to learn about the research projects of others attending the course!
A year ago today, we kicked off our first virtual course; Starting single cell RNA-seq analysis. This course was originally planned to take place onsite at EMBL-EBI Hinxton however, due to the pandemic we swiftly had to move this to virtual. Little did we know that virtual courses would still be going a year on. We have successfully hosted just over 18 virtual courses. Looking ahead to next year, we are hoping to continue with a virtual aspect of our programme. Below we hear from three team members on virtual events and their experiences.
PHOTO: Group photo from the starting single cell RNA-seq analysis course.
PHOTO: Sarah Morgan
Sarah Morgan
Sarah has been the Scientific Training Coordinator since 2012, she manages the EMBL-EBI external user training programme, and leads our team of Scientific Training Officers. As you can imagine a year ago was a very busy time for Sarah moving a full programme of courses to virtual. She tells us her thoughts and experiences of virtual courses
How did you manage the team moving into a virtual environment?
The first thing I did was check that all my team were fine working from home and getting to know their home situation – juggling children, partners, parents, pets, they had lots to deal with alongside trying to find new ways to keep delivering our programme! The move to home working was incredibly quick, so there was lots to deal with. Trying to get regular catch-ups across the team was incredibly important – I missed my daily catch-ups with our Events manager Charlotte Pearton (who I normally share an office with), and we needed to be in contact very often in those early days.
How did you manage moving an onsite course to virtual within a couple of months?
We were lucky in that we had some experience of delivering training virtually, but not to the extent that we have done over the past year. We quickly set up a small task force to plan out how we could approach delivering the courses, thinking about what platforms to use, how we would give trainees compute access, what additional support they might need; and how to encourage and support our trainers to do their job in this new environment. We spent a lot of time communicating with participants, trainers and colleagues across EMBL in the early days, and were generally met with very positive responses. The team as a whole worked brilliantly to bring those first few courses online. The support and enthusiasm from everyone is what enabled us to move so quickly, along with fantastic ways to bring the virtual training alive.
How has your job changed with the team moving to virtual courses?
I think I re-worked our training calendar about once a month from March onwards last year! Many parts of the job have not really changed that much – I still work closely with my training officers and the rest of the training team to get our courses up and running, monitoring how the courses are running and looking to improve where we can. What has changed is the travel and meeting with colleagues from across the world – though I don’t miss airports at the moment!
What do you miss most about on-site courses?
Getting a chance to see the trainees in one big group and hearing the buzz of a course in action. When courses are running in our building at Hinxton there is always a nice hum of activity at coffee and lunch breaks with people chatting and getting to know each other. I miss seeing that and getting a chance to pop down and say hello.
What is something that can never be as good as during on-site courses, in your opinion?
Dinners at Hinxton Hall (and the tea-time biscuits with afternoon coffee!).
How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts?
I would like to see a return to on-site training, but virtual courses are very definitely here to stay. We have seen some major advantages of running virtual courses, and I think looking ahead the EMBL-EBI programme will definitely be a mixture of both approaches.
PHOTO: Marina Pujol
Marina Pujol
Marina joined the team in June 2018 as one of our Events Organisers. Her focus is on our onsite and virtual training courses as well as assisting with the delivery of events for the CABANA project. Marina was paramount in the planning and delivery of the Starting single-cell RNA-seq analysis course in 2020 and below she shares her experiences, lessons learned, and tips for organising a virtual course.
How does organising a virtual course compare to organising an on-site course?
The first few months that we were organising virtual courses I thought that there wasn’t much difference between an onsite and a virtual course, however looking back at what has now been now 1 year, I have come to realise that it’s a completely different world.
Back when we worked on face-to-face courses we would deal with the logistics and organisation outside the training room, now we are sitting with them during the training too. This means our role has evolved and we have had the chance to understand and help to improve the trainers and trainees’ needs during that part of the course as well.
Events’ Organisers in the EMBL-EBI Training Team are nowadays working hand in hand, more than ever with the Scientifics Training Organisers. We are now invited to participate in the pre-organisation meetings with trainers and can provide advice thanks to our vast experience on virtual courses during the last year.
Overall, I believe this experience has enriched our job and is definitely something I would love to be part of in the future despite going back to face-to-face courses.
Top 3 tips to keep in mind while organising a virtual course?
Make the instructions on how to access the course are as clear and easy as possible, for example, zoom links, handbook link and programme information.
If possible, have at least two big screens to work like a pro, a speedy mouse, and a nice audio setting. Events’ Organisers have to juggle with at least 3 different platforms while hosting a course.
Surround yourself with amazing colleagues and team players that can give you a hand whenever you need it. And don’t forget to have something to drink and snacks available.
What is the biggest lesson you learned about organising virtual courses?
How grateful people are to be able to access training without having to travel, which would have resulted in higher costs for them meaning they might not be able to attend.
When we have delegates that are in a completely different time zone, and you can see the effort they are making to be awake and participate during the course – this makes me realise the importance that our training has for them and that we are lucky to contribute and help, even in the smallest part.
The one thing that you wished someone had told you before organising your first virtual course?
How exhausting it could be! Especially during the first courses, when everything is new and you still don’t have the hang of it. I remember being really nervous at the beginning, a lot of new information was in our heads. Now it has become the norm and it’s nice to see the progress we have made.
How does the contact with speakers, organisers, and participants differ from on-site courses?
The contact before the course is more or less the same, as we usually contact them only by email. However, once the course is running the dynamic changes quite a bit. You no longer can have that random conversation with them on their arrival or during coffee breaks, which I miss.
What is something that in your opinion is better about virtual courses?
The fact that our training can reach people from all over the world now, offering cheaper fees and even sometimes free courses that have been streamed live online. An ideal future would be to have both, virtual courses and face-to-face courses available, so more people could benefit from our training.
What do you miss most about on-site courses?
I miss the interactivity with trainers and trainees. Knowing how they are feeling daily, being able to help them with any query during the day, and having that personal contact. Although we offer a range of virtual networking activities we can never replace in-person interaction. It is also nice to see the relationships created at each course with the delegates, I believe good friendships have started in our courses.
How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts?
I would love to be able to offer both, on-site courses and virtual courses, so you have the opportunity to visit us onsite and have that face-to-face interaction but also you can choose to stay at home and have a great learning opportunity at less cost.
Hybrid at the moment is an unknown type of course for me, however, something that we are exploring in the team.
Alexandra Holinski
PHOTO: Alexandra Holinski
Alexandra (Alex) joined the team in 2017 as a Scientific Training Officer and is responsible for designing, developing, and delivering several on-site and virtual courses. Alex together with experts from the BioModels team ran the Mathematics of life: Modelling molecular mechanisms virtually in October 2020 which, was the first edition of this course. This is running again in September and is open for applications until July, find out more here.
How does organising a virtual course compare to organising an on-site course?
Organising a virtual course is different from organising an on-site course, a virtual course allows for more flexibility as far as the delivery of training is concerned. An example of this is the talks during a course, these can be pre-recorded and provided to course participants ahead of the course, watched during the course, or delivered live. The practicals can be run synchronously or asynchronously. This can be both exciting and an organisational challenge, especially as not one format perfectly suits all participants & trainers, and works for the content we deliver. The “how-to” has to be considered carefully ahead of the course so that the participants can have the most efficient virtual learning experience and both participants and trainers feel comfortable in the virtual setting.
How does the contact with speakers, organisers, and participants differ from on-site courses?
In a virtual course, we are missing out on the informal chats with participants and trainers over coffee, lunch, and dinner. These have always been helpful in an on-site course, to get immediate feedback about the training from participants and therefore identify challenges and reacting to these. In a virtual course, we are contactable via Slack, Zoom, and email but it is more challenging to notice certain issues.
How has your role changed with moving to virtual courses?
The overall role has not changed immensely, I still develop training programmes together with scientific experts and support trainers in developing and delivering their training. However, of course, the focus and how we do things has changed. Also, I am getting more involved in delivering training on my own, and I quite enjoy this in a virtual setting.
How does the course programme differ from onsite courses?
During a virtual course, we start the days with short morning challenges like quizzes, so that the participants start working and chatting with each other and not feeling isolated in front of their screens. In an on-site course, this happens automatically over morning coffee. Instead of an on-site poster session, we have flash talks that allow the participants to present their research and network with each other. Also, I have realised it is important to ensure that breaks are long enough for everyone to get away from the screen and stretch – this is similar to an on-site course but I feel breaks are even more important in a virtual setting.
What is the biggest challenge of virtual courses?
A virtual course is more challenging to create a sense of community, which encourages efficient collaborative learning and networking. In a virtual setting, there is often the danger that participants might get lost and feel isolated. However, there are ways that we can work to avoid this. In the virtual Mathematics of Life course in 2020, we ran group projects, in which we organised participants in small groups into breakout rooms and gave them a project to work on during the week. These groups were supported by trainers who jumped in and out of the breakout rooms. At the end of the course, the groups presented their results to all of the course participants. The participants worked very collaboratively and highly appreciated the group work, which was reflected in the feedback survey. We have also learnt that some participants continued working on their projects after the course had finished. In addition, we also ran morning challenges that participants were asked to work on together in breakout rooms. The flash talks during the week enabled scientific networking.
What is something that in your opinion is better about virtual courses?
Virtual courses can be more inclusive than on-site courses. We can easily reach people worldwide, including scientists from low-to-middle-income countries (LMIC). Virtual courses can also be easier to attend for scientists with family or caring responsibilities.
Also, since we moved to virtual courses, I have delivered more training on my own and enjoy this. I feel very comfortable with delivering virtual training and love being creative and developing training activities like discussions and quizzes using a range of interactive virtual tools.
What do you miss most about on-site courses?
I am missing the non-virtual informal chats with participants and trainers. It is great to get to know so many people from all around the world and chat with them in person.
How do you see the future of EMBL-EBI Training courses? What are your hopes and thoughts?
I am sure we will return to on-site training courses, but I do not think that virtual courses will disappear. By running both virtual and on-site courses we will be able to satisfy the diverse learning preferences of our trainees and allow more researchers to access our training.
Interested in joining one of our virtual courses, check out our upcoming courses here.
Meet Michelle, the Digital Strategy Officer in the EMBL-EBI Training team. She works with our European Commission funded projects such as BioExcel and CINECA. She is responsible for the social media and content for these projects along with organising scientific courses and conferences. Michelle has just returned back to the UK after spending 6 months with her family in Qatar due to the pandemic.
Michelle Mendonca, Digital Strategy Officer at EMBL-EBI
EMBL-EBI start date: August 2018 Number of organised events at EMBL-EBI: 12
What is your favourite place in Hinxton area?
The little nature walks spread across campus are my favourite. It is always refreshing to be able to take a break from work and be surrounded by greenery and beautiful flowers.
What is the first thing you do before a course starts and the first thing you do after a course finishes?
The first thing I do before I start a course is making sure I am well organised and I have everything I need to get started. The first thing I do after a course is finished, is to congratulate everyone on the team and have a long nap.
What are the challenges/differences of organising a virtual course?
I think one of the big differences for me is not to physically see if the delegates are finding everything alright. However, I do think virtual courses have opened up a whole new avenue for inclusivity and accessibility which means we get to reach a lot more people and that is always great.
You’ve been working from home for 13 months now; how have you adapted your role during this time?
Adapting to the new role was challenging at first and it took a while to find a new routine and way of working. I am working on developing better ways of communication to maintain my interactions with colleagues.
PHOTO: Michelle in Qatar
If you weren’t a Digital Strategy Officer what would you be?
I would be doing something in the creative or entrepreneurship field. So probably a YouTuber or a cafe owner in an alternate universe.
If you were a superhero what power would you like to have?
I love the Marvel series and recently watched WandaVision. So my superpower would be moving objects with the mind like Scarlet Witch from the show.
What is your favourite movie?
I don’t have a favourite movie but I am a big Bollywood fan, especially all the movies from the 90s and early 2000s.
If you’re looking for bite-sized learning opportunities delivered by EMBL-EBI experts, then our regular series of webinars might be just what you are looking for!
EMBL-EBI’s Training team has been running a series of webinars since 2013, featuring speakers from across EMBL and beyond. Over the years we have covered a wide range of subjects, but its roots are in the resources and databases made available by EMBL-EBI, as well as related biological topics. So far in 2021, we’ve heard from members of Ensembl, RNAcentral, EuropePMC, UniProt and the European Genome-Phenome Archive, with many more to come.
The webinars were started as a way to enable a much wider audience to access our training and interact with our experts. They provide attendees with an introduction to a topic and resource, along with the all important opportunity to ask questions directly to our trainers. If you want to know more about how to use a resource, or perhaps how to analyse or submit data, these are the people with the answers!
Exploring our upcoming webinar listings provides an overview of subjects to be covered. For the majority of webinars the only thing required is an interest in the topic, though some may be aimed at a more specific audience.
The Training team’s Scientific Training Coordinator, Sarah Morgan, at the first webinar of 2021, introducing EMBL-EBI’s resources and the training available.
The series is currently organised by my colleague Ajay Mishra and I. One of us is on hand at every webinar, introducing the speakers and making sure everything runs smoothly. As well as ensuring questions are answered, we also provide an opportunity for all attendees to give feedback, so if you join us, please let us know what you think. You can also tell us if there’s a topic you are keen to see covered in the future.
EMBL-EBI’s webinars are currently run by Anna Swan and Ajay Mishra.
Over the years we have run a number of focused webinar series, including programmatic access of EMBL-EBI resources and data management. From April this year, we will be running a new focused series, “A guide to…”, where we will introduce some concepts in bioinformatics and how they link to some of the EMBL-EBI resources. This series is aimed particularly at students and early-career researchers, but anyone with an interest will be welcome. We will be kicking off the series with topics such as “A guide to exploring genes and genomes with Ensembl” and “A guide to RNA families”. The first webinars in the series are available for registration now, but keep an eye out for future topics in this series, including drug discovery and pathway analysis.
If you are ever unsure about joining a webinar, you can always contact the team at webinars@ebi.ac.uk and we’ll happily answer any questions you may have. We’re also always thinking about what to include next in the programme, so let us know if there’s something you would like to see.
Finally, if there is a webinar that has taken place in the past or there’s one you cannot attend, it is not a problem! We record them all and make them available, along with the slides, in the on-demand section of our website. We always include details on how to get in touch with the trainers and their teams so you can ask the experts a question anytime. We also encourage other trainers to use our recordings and materials in their own training – check out these details on re-use of our content for further information.
We look forward to seeing you at a webinar in the future.
Written by Anna Swan.
Anna Swan – Scientific Training Officer (e-learning) – EMBL-EBI Training
Anna joined the Training Team at EMBL-EBI in March 2019 as a Scientific Training Officer (e-learning). She has a PhD in Bioinformatics from the University of Nottingham, where she focused on the bioinformatic identification of biomarkers of osteoarthritis. Following her PhD, Anna worked as a medical writer, spanning many therapeutic areas and working both on promotional and educational content for clinicians. Returning to bioinformatics, Anna worked as a data wrangler for the International Mouse Phenotyping Consortium at the project’s data coordination centre based in the Medical Research Council’s Harwell Institute.
