Meet the EMBL Events Team: Jane

PHOTO: Jane Reynolds

Today’s interview is with EMBL-EBI’s Jane Reynolds. Jane is one of the event organisers in the team, and joined in December 2020. Jane’s focus is on the on-site and virtual training courses.

At EMBL since: December 2020
Number of organised courses: 1

 Favourite place in Hinxton area? Having joined EMBL-EBI just before Christmas, I haven’t been able to explore Hinxton yet. I did enjoy a virtual tour of the conference centre though, which gave me an insight of where the course dinners take place.

What is the first thing you do before a course starts and the first thing you do after a course finishes? Before an event starts, I remind myself of the hard work and preparation that’s already been done and that the best thing I can do from here on in is be present and ready to deal with anything that might arise. After an event finished? Well, it sounds a bit dull but I usually make a quick list of things that could be improved (as well as those that went really well). Particularly working in new formats, it’s often only by running an event that you notice the small changes that can be made to improve the experiences of delegates or speakers. I like to capture these while they are fresh in my mind.

What are the challenges/differences of organising a virtual course? One of the major changes has been how big chunks of work have shifted closer to the start date of an event; for example, delegates tend to sign up later to online events than in-person events, even if they are advertised for the same length of time as usual, so the timeframe for dealing with the administration related to this is shorter.  The work definitely has a different rhythm to it and the tools and systems have changed but the reason we’re doing it is the same.  Remembering this has helped me to adapt.  Although I have to say I am really looking forward to meeting delegates (and my new colleagues!) in person when the time comes.

You’ve been working from home since you started your role at EMBL-EBI; how has this been for you? As well as working from home, I’ve been lucky enough to start a new role in the past year, and it’s been an interesting (hopefully once-in-a-lifetime!) experience.  Luckily the Training Team at EMBL-EBI have been wonderful in sharing their knowledge with me and given me a very warm virtual welcome.

If you weren’t a EMBL-EBI events organisers what would you be? Probably a teacher of some kind.  Before I started working in events and engagement, I worked as an English Language Assistant, which I really enjoyed, so ideally I’d combine teaching and travel.

PHOTO: weekend city break in Copenhagen May 2020

What is the strangest/funniest thing that has ever happened in a course? My birthday is in July and in my past jobs this has been the busiest time – either at Graduation events or summer events – so I have often spent it working, but never in an office!  I’ve been organising table plans in Liverpool Cathedral, at a Massive Attack concert in a disused train depot or hosting tours of new exhibitions…one of my favourite things about working in events is that there is rarely a dull moment!

If you were a superhero what power would you like to have?  I love learning languages but it’s hard to find the time…so definitely the ability to speak and understand different languages without having to learn verb tables!

What is your favourite TV show? Like everyone I’ve watched a lot more TV than usual over the past year, but The Sopranos – which has stood up to a rewatch or two – remains my favourite.

Upcoming events that Jane is organising: Cancer genomics 2021 – virtual 

Why do we charge registration fees for virtual events?

“Why do you charge registration fees for virtual events? You are not flying speakers in, there are no accommodation or catering costs. You are not printing any conference material!” Yes, you are absolutely right! All of these are valid points in the world of virtual training. And yet we are still charging registration fees. Why?

As a non-profit organisation and with training being one of its five missions, EMBL sets its fees at the lowest possible level to just cover the costs of the events program. These are:

Staff

It sounds incredible, but virtual events turned out to be more time-intensive and demanding in terms of staff support than we thought. We are now busy scheduling test runs with speakers, populating virtual platforms, coordinating the timely and high-quality delivery of pre-recorded talks, providing technical support and trouble shooting – all things we didn’t have to do for onsite events, or previously had support with from our onsite service staff. In the past year, our team has even grown in order to be able to deliver the 31 virtual courses and conferences that took place in 2020.

Behind the Scenes at the EMBL Conference: Transcription and Chromatin (27 – 29 August 2020). Previously only one conference officer was the main coordinator of an onsite meeting. Now there are always two people onsite, splitting the tasks of monitoring and communication with the participants, speakers and audio-visual technicians.
Software

Unfortunately, virtual events cannot be run solely on Zoom. That would have made everything much easier, but attending a conference or course is so much more than listening to the talk. Participants look for interaction, networking options and avid peer exchange. So our courses’ and conferences’ programmes incorporate a range of networking and knowledge-exchange sessions such as meet-the speakers, bar mixers, pub quizzes, speed networking and poster sessions. In order to meet these requirements we make use of paid solutions which offer all these benefits and are easy to navigate for the users.

Training

New software means new set up in terms of design and maintenance, and to make sure everything runs as smoothly as possible during the events our staff require appropriate and sufficient training to be able to operate it.

Sponsorship

With all our events turning virtual, income from sponsorship has decreased accordingly. Normally at a conference you would see several companies exhibiting in the Advanced Training Centre foyer, but with the meetings taking place entirely online, there has not been as much interest in virtual sponsorship. While we are being creative with what we can offer our sponsors, they also miss the face-to-face interaction with our participants.

Marketing

While the onsite costs have decreased, getting the word out still requires the same amount of budget (if not more!). How do we make sure you hear about us and the virtual meetings we are organising? How do we stand out from the other virtual events that are currently out there? Would you hear about our meeting if we used the traditional channels as before? In most cases, we have had to add on to our marketing channels and campaigns to increase awareness about our virtual programme.

Fellowships

EMBL offers various types of fellowships to support scientists to attend our events. An advantage of the virtual format is that with lower registration fees and no travel to cover, the funds stretch much further.  We are finding that we are able assist more applicants than ever before to attend entirely free of charge.

 

The smarter way to find bioinformatics training

The EMBL-EBI Training website is the first port of call for many life scientists, bioinformaticians and computational specialists looking to further their knowledge of the field. We’re proud to offer world-leading bioinformatics training to users across the globe, with over 600,000 visitors to our online courses alone each year.

Now more than ever before, we see the need to make our training easily accessible, visible and findable so that anyone, regardless of location, career stage or experience of training with us can find the resources they need.

We’re therefore very pleased to be able to introduce to you the brighter, smarter way to find bioinformatics training from EMBL-EBI.


What’s new?

  • Find relevant training more easily, in the format that works best for you 
  • Flexible free-text search based on EMBL-EBI’s own search engine 
  • Combine search and filters to quickly identify the course you need 
  • A modern, clean look and feel with simple navigation 

Site tour searching our virtual courses

Site tour searching our recorded webinars

How did we do it?

This project officially began in April 2019, when we discussed the brief and set things in motion for the next 12-18 months. Little did we imagine that an idea sketched out on a plane journey from London to Amsterdam in early 2019 would lead to such a large scale project. We constantly review our engagement with users and potential trainees, enabling us to think about how we can better provide the content and course information they will be searching for. This in turn enables us to remain world-class leaders in what we do. From the start we were led by user feedback and web analytics in order to define where improvements were needed.

The main purpose of this project has always been to enable and encourage you (our users) to engage with all our content and put the training into your (virtual!) hands.

We needed a new interface that works for a diverse user base, regardless of research needs, scientific interests or career stage. Given that we offer a mix of live training and on-demand content (freely accessible, anytime), this was always going to be a task requiring a lot of man-power from across the organisation to make it the best it could possibly be. 

Team creation and adoption of agile methodology

Our ongoing collaboration with the EMBL-EBI Web Development team has been crucial to getting us from concept to a final product. They have not only provided us with several talented developers who make our ideas come to life on the web, but also user experience (UX) experts, who have helped us explore what our users really need. 

We began the project with a plan to implement agile scrum methodology as our guiding framework, which was new to many members of the project team. As such we worked in two-week ‘sprints’ where the team would focus exclusively on the project, maximising efficiency and creating a potentially releasable product at the end of each sprint. 

First steps

Our first task was to redesign the courses in our Train Online catalogue, our freely-available library of online tutorials. We took one of our most popular courses, called Bioinformatics for the terrified, and soon released a live BETA version for our users to try out and provide feedback to guide us as we worked on other course types and pages.

If you have used our website regularly, this image will look pretty familiar to you. This is what the team started with at the beginning of the project.

We then moved to this updated design which you can see looks very different from our old course pages. This is where the design really took off and we used this as a base to make other minor changes which took us to our final design which you can see below.

Here it is, our final design. The layout and functionality remained largely the same from the first design based on user feedback, but we updated the graphics which you can see in the page header. Read more about the background behind the graphic changes below.

Design 

The users and the EMBL-EBI training team gave very positive feedback on the layout and functionality of the new online course pages. However we quickly realised that we required some design expertise and our colleagues at EMBL Design were brought on board to assist with providing beautiful new graphics for the page headers. We also utilised the EMBL visual framework to create a look that was coherent and consistent with other pages in the wider EMBL brand. The EMBL visual framework is what provides the building blocks of this new look and feel.

New event pages

We followed up the creation of the online courses by implementing similar design and layout changes to our live courses. We gradually began to make the switchover with both upcoming live events and our extensive back catalogue of on-demand materials.

What’s next for the project?

Two years on, the whole of the EMBL-EBI Training site has been redesigned and deployed following an iterative and user-centered approach. We are thrilled to be able to release this to you – our users – so you can benefit from the new look and functionality.

Our hard work doesn’t stop now. Next up, we will be looking to enhance your experience even further by enabling you to track your personal progress, and enhancing the way you access past content to help you continue your learning journey with us.

Acknowledgements

We’d like to thank all those that have been involved in this project from across the EMBL and EMBL-EBI teams, as well as you (our users) that have feedback across the journey. 

Special thanks go to Adam Broadbent, Ajay Mishra, Anna Swan and Sarah Morgan from the EMBL-EBI Training team, to Nikiforos Karamanis and Prakash Singh from EMBL-EBI Web Development team, and to past team members Melissa Burke and Joseph Rossetto – without you, this project wouldn’t be the success it is today.

Photos from the project

Here are a few snaps from the project along the way.

One of the first sketches of the cover page of the online tutorials.
A wireframe with notes after a feedback session.
One of our many higher fidelity mockup with feedback from a usability test: Green sticky notes report positive feedback (but there are some remaining issues).
Here we have Jonathan Hickford (previous Head of Web Development) and Sarah Morgan (Scientific Training Coordinator in the Training team) writing user stories.
When we got to the end of a sprint there was only one way to celebrate…cake.

Meet the Trainers – Tobias Rausch and Alexey Larionov

On the occasion of World Cancer Day (4 February), we meet two of the trainers of the virtual EMBL Course: Cancer Genomics  (17 – 21 May 2021) – Tobias Rausch and Alexey Larionov.

PHOTO: EMBL Photolab

Tobias Rausch (TR) received his PhD in “Computational Biology and Scientific Computing” at the International Max Planck Research School in 2009. He then started to work at the European Molecular Biology Laboratory (EMBL) as a bioinformatician. His primary research interests are population and cancer genomics, structural variant discovery and omics computational methods development. (https://github.com/tobiasrausch).

 

PHOTO: Alexey Larionov

Initially educated as a clinical oncologist in Russia, Alexey Larionov (AL) switched to  experimental oncology upon completion of his PhD. Initially he worked as a postdoctoral researcher in Edinburgh University studying transcriptomics of breast cancer, with a focus on markers and mechanisms of endocrine response and resistance.  Working with data-rich methods (qPCR, micro-arrays, NGS) he became interested in data analysis and switched to bioinformatics. Since completing his MSc in Applied Bioinformatics, Alexey has worked as a bioinformatician at Cambridge University, focusing on NGS data analysis and heritable predisposition to cancer. See http://larionov.co.uk for more details.

What is your research focus?

TR: Computational genomics.

ALHeritable predisposition to cancer

Why did you choose to become a scientist?

TR: When I started at EMBL I saw myself as a software engineer who loves to design, develop and implement algorithms to solve data analysis problems. With the advent of high-throughput sequencing, this engineering background gave me a competitive edge as a data scientist, and that’s how it happened!

ALIt was interesting…

Where do you see this field heading in the future?

TR: Nowadays cancer genomics is a data-driven team science, but it is a long way from obtaining data to obtaining insight. In the age of analytics we all have to wrap our heads around multi-domain data with spatio-temporal resolution, ideally in real-time.

AL: I assume that the question is about translational cancer research in general.  I expect that in the near future the field needs better integration of different types of biological data and better collection of relevant clinical data. 

How has training influenced your career?

TR: I think training is essential to get you started. Training is like a kind person who takes your hand and guides you through unknown territory. It goes along with mentorship and I was lucky enough to have good training and good mentorship already as a student.

ALSince my initial clinical and bioinformatics degrees, cancer research has changed so much that I would not be able to even understand current papers if I hadn’t taken regular in-depth training in different aspects of computing and bioinformatics. 

How has cancer research changed over the years?

TR: I hope I am still too young to answer that :-). I leave that question for Bert Vogelstein or Robert A. Weinberg.

ALCancer research has become much more complex and powerful because of the development of new methods; specifically significant progress in bioinformatics, sequencing and human genomics.

Which methods and new technologies will be addressed in the course?

TR: We try to give an overview of how high-throughput sequencing can be applied in cancer genomics. We cover a range of technologies (short-read and long-read sequencing), data types (RNA-Seq, DNA-Seq and ATAC-Seq) and data modalities (bulk and single-cell sequencing), and last but not least – we take a deep dive into cancer genomics data analysis.

ALIn my sections of the course, I will discuss established methods for the analysis of bulk RNA sequencing, focusing on differential gene expression.  Then I will touch on the new methods being developed for the analysis of long-read RNA sequencing.  

What learning outcomes should participants expect to take home after the course?

TR: To come back to my previous answer: I hope after the course, cancer genomics won’t be an unknown territory anymore for the participants. I hope we pave the way and then it’s up to the students to make something out of it.

ALIn my section of the course, participants will learn:

1) Bioinformatics algorithms and tools for QC, alignment, and gene expression measurement in bulk short-read RNA-sequencing data

2) Current approaches to analysis of long-read RNA-seq data, comparing the Oxford Nanopore and PacBio sequencing technologies.


Interested in this course? Apply by 26 February.

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

‘From Functional Genomics to Systems Biology’ shines virtually

Event report by Jesus Victorino, PhD student at the Universidad Autonoma de Madrid, Spain.

Four Novembers ago, I arrived in Heidelberg on my 24th birthday which I celebrated carrying my first poster as a freshmen PhD student. Back in those days, a hypothesis with an outline of my future experiments was all I captured on that A0 laminated fabric poster. Four years and a PhD later, there could not be a better place to show my results right before defending my thesis than at the very same EMBL conference: From Functional Genomics to Systems Biology. Well, not exactly the same. This time we could not enter the ATC building and walk through its double-helix bridges, since the event took place virtually.

The organising committee managed to set up an online conference, enabling more than 270 participants to share their thoughts and results about genomics, proteomics and imaging. And we got to see everybody’s living room! Although the schedule differed from usual conferences in Europe (13:00-20:00 CET), it broadened the audience by allowing people from other countries to attend. And all that without taking a plane or paying for a hotel room, which significantly decreased the required budget to attend the conference and the carbon footprint we left behind.

I found several additional aspects of attending a virtual conference very exciting. On the one hand, the lack of big crowds in a large room with a single microphone and a line of researchers waiting for their turn, encouraged me to ask questions to the speakers. I simply felt more comfortable. Zoom allowed a record of the many questions asked, and those that were not answered due to time constraints were posted on a Slack channel created to coordinate the meeting. The Slack channel was incredibly helpful not only to increase the feedback with more scientific questions & answers but also to improve networking, especially for the poster session. I hope we keep using a similar virtual space that enables participants to contact other scientists even for onsite conferences.

At least in my experience, the poster session worked out way better than expected, which was a pleasant surprise. I found myself talking with researchers (mainly PhD students) for most of the session, which I never experienced before. I took advantage of the Slack channel to advertise my poster and also to interact with the presenters of other posters I was very interested in. Magically, people were showing up in my Zoom room and I found that breaking the ice virtually was easier than in a real room, since there was no awkward moment in which you hesitate to interact with the presenter, or the presenter does not know whether you might want to know more about his/her research or are just passing by.

On the other hand, I found the platform where we should upload the posters very inconvenient. Instead of uploading our posters in PDF and being able to chat through Slack, Zoom or similar, we had to use ‘iPosterSessions’ and re-shape our posters to fit the virtual and very rigid format of the website. I found the platform non-intuitive and there were incompatibilities, at least with my computer, for the ‘chat’ and ‘contact author’ options within it. Besides, we had to provide a way to virtually meet other participants and present our posters on our own (e.g. a Zoom room or similar), which was not very straight-forward,, and not everyone might have had access to it. Having said that, this was basically the only issue I experienced during the entire meeting – the lectures worked perfectly, we discussed exciting projects and the poster sessions were very fruitful.

Another great choice from the organisers was to schedule ‘meet the speakers’ sessions. I enjoyed meeting three of the speakers together with other early career researchers where we could exchange thoughts and impressions. I think this is very important to train students on how to interact with more senior researchers and I have rarely found a dedicated spot for this at international conferences.

During the conference, all lectures and short talks were divided into four main thematic areas: quantitative genomics, quantitative proteomics, quantitative imaging and single-cell genomics. Here’s my pick from the panel of speakers that I feel represents the essence of each area.

Transcriptional enhancers were the main characters of the quantitative genomics sessions, where different labs addressed the question of how the control of gene regulation affected phenotype in a different way. The fruit fly embryo was one of the preferred model organisms and was used by the team led by Thomas Gregor to study how the spatial organisation of the chromatin affects transcription at the eve locus. Justin Crocker also showed beautiful Drosophila embryos that they used as a test tube to understand the logic of a developmental enhancer and the phenotypic impact of its mutations. With respect to this study of the genotype-to-phenotype impact but in the context of human genome variation, Bart Deplancke told us about how non-coding variants affect gene expression in immune cells unveiling implications in leukemia.

Following with genomics, we witnessed the power of sequencing technology but at the single-cell level to understand physiology and disease. In this thematic area, we learnt with Antonio Lentini about gene expression and silencing at the X chromosome and Dana Pe’er talked about its uses to study development and cancer. The work presented by Henrik Kaessmann was very impressive and stood out not only for the use of thousands and thousands of cells, but for studying spermatogenesis in twelve different mammals providing a valuable resource to study this process across evolution.

The quantitative proteomics sessions taught us about the promising years that we face since improved technology might quickly move the field forward. Bernhard Küster showed how proteomics and in vitro models can be used to investigate drug response to cancer treatments. Although the massive characterisation of the proteome is yet not comparable with the performance of sequencing technologies in the genomic field, Michiel Vermeulen’s talk illustrated how to combine genomics and proteomics to understand cancer biology and identify new important players and therapeutic targets.

The fourth thematic area was quantitative imaging in which Emma Lundberg talked about high-throughput imaging and its use to dissect the human proteome. We could appreciate the potential of the analysis of massive amounts of imaging data in the work presented by Professor Lundberg where they involved hundreds of new proteins in cell cycle and identified new putative roles for proteins they found to localise in multiple subcellular compartments. Super-resolution microscopy could not be missing at this conference and Suliana Manley nicely showed how to use it to study mitochondrial organisation and dynamics.

Outstanding science and fresh data in a very interactive environment summarises the experience at the conference, where I was glad to see that many of the projects presented were shared in the form of preprints. I collected them and included in this list of preprints at the #EMBLOmics for attendees who might want to know more about some of the talks and for those who did not attend and might want to have a flavor of this conference.

Of course, it would not have been a proper EMBL meeting without the final gathering and concert. The event ended with a fantastic concert by Lazy Fur which really put the icing on the cake –the concert is recorded here, so you can listen to their nice voices while you prepare for your next experiment. I really thank the organisers for all the effort to make the screen disappear and feel like in a non-virtual event.

Since 2020 has shaken the way we interact with people, scientists, like everyone else, have had to quickly adapt to the new circumstances. In the academic world, conferences play an important role for scientists to share their recent advances and build their contact network. While it was already under debate how to reduce the ecological impact of such a tremendous flow of researchers travelling all over the world, virtual conferences did not seem to launch. All of a sudden, the global pandemic situation has rapidly turned this will to a necessity, leaving us no other option but to evolve. The good thing is that virtual conferences seem to be reasonably meeting our expectations, providing with a more sustainable way of sharing our data and interacting with each other. They offer both advantages and disadvantages with respect to in-person events but undoubtedly have accelerated our steps towards including more virtual conferences in the calendar once we go back to a ‘normal situation’.

 About the author

I’m Jesus Victorino, PhD student working in gene regulation and member of the preLights community, a platform to disseminate science and the role of preprints in Biology.