Meet the Trainer – Jonathan Manning

PHOTO: Jonathan Manning

The Introduction to RNA-seq and Functional Interpretation course (21 – 25 February 2022) is now open for applications and we thought we would introduce you to one of the course trainers, Jonathan Manning.

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!


Interested in this course? Apply by 12 November 2021

For more upcoming events on cancer research take a look at our event listing.

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Meet the Trainer – Varsha Kale

PHOTO: Varsha Kale

Meet Varsha Kale, a Bioinformatician in the Finn team: Microbiome Informatics at EMBL-EBI and one of the trainers at the EMBL Course: Metagenomics Bioinformatics (08 – 12 November 2021).

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!


Interested in this course? Apply by 03 September.

For more upcoming events on cancer research take a look at our event listing.

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From an online interview to running my first virtual course

Iva Gavran joined the EMBL Course and Conference Office in December 2020.

We asked Iva Gavran, who recently joined the team as a Course and Conference Officer, to give us her newcomer’s insights about the very first virtual course she organised (EMBO Practical Course: Drosophila Genetics and Genomics, 11 – 15 January 2021), held in the EMBL virtual learning platform – eCampus.

It was December 2020 and after a 5-day quarantine and a PCR test I had started working at EMBL. It was just one month before the EMBO Practical Course: Drosophila Genetics and Genomic was scheduled to take place. A virtual course, of course.

In fact, my job interview at EMBL was held virtually as well and I had seen the EMBL ATC building and the city itself only in pictures prior to relocating to Heidelberg (and oh, both are stunning).

A lot of things for the course were pretty much arranged by then, but I was still baffled about how one could organise a virtual practical course. The answer may well lie in the EMBL Advanced Training Centre building’s architecture that resembles the DNA’s double helix and reminds us that adaptation is the key. We have fully adapted the face-to-face training’s structure and interaction to a new, online format.

Virtual platform

What really helps is that there is a whole learning platform dedicated to our courses, called eCampus. A clean slate at first, it was soon populated with all kinds of learning materials, videos, articles and other input sent by the speakers and trainers.

The EMBL virtual learning management platform eCampus was launched in 2020 and is used as a collaboration and networking tool by the virtual course participants.

Course materials and programme

I would say there are three main pillars of eCampus: the pre-course materials, the interaction options and the daily programme. The pre-course materials are a proper little treasure trove of knowledge with pre-recorded videos, quizzes, articles and assignments. If you have any questions, just go straight to the Forum and ask away, or chat with another participant or trainer. The programme is always up-to-date with all the links you need and it also has a nice feature where you can adapt it to your time zone. If a live session has some pre-course materials that need to be watched or read, it will be hyperlinked in the programme or the material will be added below, which is pretty cool and very convenient.

Networking

Networking is a crucial part of every event, whether it’s a conference or a course, but it is hard to replicate in a virtual environment. I remember how it was for me to virtually meet my colleagues, and trust me, it’s definitely odd, but somehow at the same time it also felt normal. After all, we share the same work experience and it’s the same when attending a course. Well, not exactly the same if you are a work-from-home parent, but EMBL has amazing childcare grants to help you with that.

The Drosophila course started off on a Monday with an ice breaker event, where all participants shared a few slides to introduce themselves, their hobbies and their career path. It was a full display of lockdown life with cooking, baking and Netflix all over the slides (mine included). There were also networking activities like speed networking, student presentations, a discussion panel and a quiz which fostered interactions between participants and trainers and helped create a really nice group dynamic.

Course modules and learning process

The course was designed in a way that required some pre-course work.  The platform contained a lot of pre-course materials, papers and videos which the participants needed to go through before attending the full 5-day course with about 4-5 course hours per day.

I remember some participants were a bit unsure if they needed to watch them before the course. The idea (and I really liked this) was that participants watch the pre-recorded videos in advance, so that when the speakers and trainers joined live during the course, participants could ask as many questions as possible and thus learned even more from the discussion. This was actually the true benefit of the virtual course – a more thorough discussion and full understanding of the topic compared to the standard format of live lectures followed by 5 min of Q&As. And judging by the participants’ feedback, this format was quite a success.

Some of the interactive sessions of the course were designed in a similar way. For example, participants were assigned tasks that they had to complete before the course. During the course, they received feedback, could ask questions and go over the rest of the tasks with the trainers. To let this all sink in properly and to give them a chance to reflect on what they had learned, participants were able to access all the materials and live recordings for two weeks after the course. As some pointed out, this was amazing for a virtual event and I agree completely.

For me, the best part of the Drosophila course was watching the lively interactions and discussions between participants and trainers, and especially among participants during their presentations of their current research. I found it inspiring and rewarding to see their curiosity and ideas. There it was, 20 people sitting in their homes in different parts of the world, talking about one tiny fly with top experts in the field. How amazing is that!

Events Iva is organising or co-organising:

EMBL Course: Advanced Fluorescence Imaging Techniques, 23 – 27 August 2021

EMBL Course: Gene Expression at Spatial Resolution, 30 Aug – 2 Sep 2021.

EMBO | EMBL Symposium: Seeing is Believing – Imaging the Molecular Processes of Life, 5 – 8 Oct 2021.

EMBL Science and Society Conference: One Health: Integrating Human, Animal and Environmental Health, 3 Dec 2021.

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Lazy Fur upgrades virtual conference experience with live music

Meet Ira and Tom – a newly-wed couple from Heidelberg and band members of Lazy Fur – a music duo that have been performing live for participants of numerous virtual EMBL conferences and symposia.

Tom and Ira of Lazy Fur. Ira holding a mic, Tom playing the guitar
Tom and Ira of Lazy Fur

“It feels good that we can bring joy and help provide even a better conference experience with a little bit of live music.”

Who is Lazy Fur?

Tom is a Research Staff Scientist in Matthias Hentze’s and Wolfgang Huber’s labs at EMBL Heidelberg and Ira is an executive assistant in a real estate company.

Both of them grew up with music. Ira started singing when she was little and now also plays the piano and bass guitar.

“I used to play the keyboard but discovered my calling as a guitarist in my PostDoc time at EMBL.” Tom shares.

They bonded over their passion for music and started playing acoustic covers of pop and rock songs and singer/songwriter style music. Ira is inspired by Walk Off The Earth, a Canadian group of friends who do spectacular covers of pop songs. And Tom is generally fascinated by buskers in Dublin he met during his PhD.

Virtual concert setup

Virtual conferences are great for many things, but it is very hard to organise entertainment. Lazy Fur found a way to give a live music performance and interact with participants.

Tom had to put in quite some effort to get it right:

“The technical side was quite challenging at first, but now we are very happy that we can provide high-quality streams. We can interact with the viewers who appreciate the live aspect of our performance. ”

What is it like to perform for a virtual audience?

Onsite, you can easily tell which songs the audience likes and if they like the show. In front of a virtual audience, it is more difficult, because you can not see and hear them. Tom and Ira did find a way to interact with the audience.

“The audience can communicate with us either via the YouTube or conference platform chat displayed on the TV in front of us.” Tom says. 

Ira: “We are extremely happy about all the positive responses we got in the chat or comments people sent us after the show.”

Tom: “We have had heart-warming messages from participants about how they enjoyed it. They wrote that this was a very unique and uplifting experience that reminded them of past conferences at the EMBL Heidelberg site.”

And after Covid-19?

Tom: “Performing live is just an amazing experience. EMBL has a great appreciation for live music at their events and it is wonderful to connect with people on that level. So yes, definitely looking forward to that as well!”

Lazy Fur will be performing at the virtual EMBO Workshop: Predicting Evolution, 14 – 16 June 

Check out the website of Lazy Fur
Check the Lazy Fur YouTube channel

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EMBL-EBI Training – 1 Year of Virtual Courses

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
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. 

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