In Focus: EMBL-EBI Training

In 2019 EMBL-EBI celebrated their 25th anniversary. To commemorate this milestone, a series of videos – In Focus – were filmed, including one with our very own Cath Brooksbank, Head of Training at EMBL-EBI.

In the video, Cath discusses the role of technology in bioinformatics training from past to present and through to the future.

Traditionally bioinformatics training has been face-to-face, but EMBL-EBI also have a large online training offering through our Train Online programme.  Train Online can be remotely accessed around the globe, at anytime, allowing our training to reach a much larger global audience at a time that suits the user.

Train Online is currently undergoing a makeover – check out the new look at bit.ly/betaBix

At EMBL-EBI we also want to breakdown the isolation faced by solo bioinformaticians in institutes, and bring them together with peers through our training offering – whether in person or online via collaborative tools such as Google Docs.

And of course there will be times where face to face will not be possible. Whether due to ill health, parental leave or visa issues we understand that sometimes people cannot physically reach our on-site training courses. For those times, we have our robot avatar to enable remote access to our events. Read more about our robot.

EMBL-EBI Robot Avatar facilitates remote learning

Check out our range of online courses; access anywhere, at any time.

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How can conference exhibitors and sponsors help your research?

Matthias with several participants from the EMBL Conference: Transcription and Chromatin 2018. From left to right: Adam Whisnant (University of Würzburg), Melvin Jesus Noe Gonzalez (Francis Crick Institute), Matthias Spiller-Becker (Active Motif Europe), Gabriel Villamil (Max Planck Institute for Biophysical Chemistry). PHOTO: EMBL Events

Meet Matthias Spiller-Becker, Key Account Manager at Active Motif Europe. Matthias acquired his PhD degree in Biology at the Centre for Molecular Biology Heidelberg (ZMBH) where he focused on chromatin and the regulation of the centromere in Drosophila. Now in his 7th year at the company, Matthias is one of the most familiar faces at our conferences on transcription, chromatin and epigenetics – always friendly and welcoming. The popularity of the Active Motif booth at these events has not gone unnoticed, so we asked him what the secret to this success is and what tips he can give to conference attendees when approaching exhibitors.

How many events does your company exhibit at annually? 

In general we participate in about 50+ conferences and meetings/workshops each year, globally. But it’s not only the big and medium-sized conferences that are important to us. We often try to be present at more intimate, local events. Sometimes we sponsor chromatin clubs where only a couple of students and postdocs come together to share their latest research. And we also do a lot of tech talks where we discuss cutting-edge techniques to study gene regulation.

In the era of digital advertising, why do you still choose to be physically present at conferences?

Talking to people face to face changes EVERYTHING!

I think that’s a statement of holistic truth in life! You don’t trust companies in the first place – you trust people. You don’t buy your antibodies or reagents from companies. You buy from people!

And even more: you don’t give away your scientific baby (aka outsourcing your project) to strangers – you give it to people you know and trust. Sure, it happens a lot that folks in the lab search an assay on the web and inform themselves about alternatives on the market before making their “informed” decision, but that is often not the end of the story. It turns out that students and postdocs mostly need to get in touch with us at some point during the experimental process to further discuss their project. And surprisingly often, this first interaction happens at conferences as in “hey, are you working for Active Motif…I think we used your antibody. Can I ask you something?…”. Moreover, being physically present at the conferences is the only way to stay current with cutting-edge research. We discuss with people at their posters and also join the conference sessions in order to see the latest and future trends in chromatin and gene regulation research.

Apart from presenting their newest technology and developments, what else can exhibitors offer participants?

Networking, distraction, fun, and a “Staun-Anlass” (hard to translate that word but probably a reason to positively wonder nails it). Basically, you want to be the red bean in a jar full of green beans. You want to be distinct and recognised among others, leaving a positive impression that lasts.

During my PhD, I always liked companies that didn’t come around too stiff at conferences, but were more approachable”. As a student it takes courage to cross the invisible boarder at a company booth – you don’t want to end up in the web of the sales spider. You are afraid that the company representative might talk you into buying something you never really wanted.

I know this feeling personally – so I try to avoid that when talking to people. My daily goal (whether at a conference or elsewhere) is to be able to help people a bit further. Having a chat at the conference booth can do many things. For example, you may learn that the problem you are discussing with the exhibiting company is indeed a bigger one that’s not to be solved easily. That’s great information! You may also hear that your problem is actually easy to address and solve – even better! You may get info about peers in the same boat as you => networking!

And last but not least, you may simply want to use the chance of talking to people in industry to get an idea about their journey in life & science => career chat!

I try to offer all the above to the people that get in touch with me during a conference!

The Active Motif booth at the EMBO|EMBL Symposium: Metabolism Meets Epigenetics (2019). PHOTO: EMBL Events
What tips can you give participants on how to approach exhibitors?

DON’T BE SHY! Just go and talk to them.

Of course, you need to choose your battles. Often it helps to orient yourself first. Do you already know the company? Is there an overlap between your research and them? If not, just read their banners and roll-ups. Sounds trivial but many people don’t do that. A company would hopefully try to have the most prominent and distinct features of their capabilities written or otherwise sketched out on their banners. If you don’t find any overlap there, I would not necessarily approach them.

But beware: company roll-ups can be like lab websites. Some truths are stated, and some are hidden, so even if your fancy new technique is not mentioned there, as long as the company topic seems to fit your science, go check them out.

If you just want a pen or some chocolate but otherwise, they don’t interest you – simply tell them upfront. You will still get your sweets but honestly, how many pens does a single person need?! 🙂

Can you give an example of a mutually beneficial collaboration that has arisen at your booth through your presence at a conference as an exhibitor?

There are so many examples. It frequently happens that conference participants approach me and tell me that they have an issue with a given technique, mostly Chromatin IP. It turns out that talking them through the experiment step by step often yields at least one weak spot in the setup.

A classic is that people often use the same amount of antibody for ChIP, independent of the varying targets and the respective antibody clones they may use. This is (like many protocol-related “facts” in the life sciences) a dogmatic – or nearly a religious – topic. People can be determined to use “always 2 µg of antibody”. Then you ask them “but did it work when using 2 µg?” and they may need to admit that “no, it didn’t”.

This is a good example that talking with a person outside your own lab can help you to critically re-consider an established protocol, and see things from a new angle.

Another example is that some projects can truly benefit from outsourcing parts of it. Everybody does it in academia but they mostly call it a “collaboration”.

You can take it a step further and outsource parts of your work to a company that offers paid scientific services. This “commercial relationship” can truly boost creativity and assay development. A company that does ChIP-Seq as a paid research service for years will always see more model organisms, more common and uncommon obstacles and more antibody targets than any other lab working only on their own project.

What approach do you use to get into contact with participants?

“It’s just me, myself and I” LOL…

No, it’s not 100 % like that but mostly…you need to simply engage the people!

I try to see every interaction with a person as the most important one in my life at that specific moment. I tend to call that my “Dalai Lama approach”.

How else can you do it!? At Active Motif, we often use our chromatin-related T-shirts to break the invisible barrier between conference audience and the booth. People usually like nerdy science shirts and ours are no exception to that rule. I mostly play a game where people can win the shirts or at least have some distraction from the packed conference program. Often, I implement a little quiz session: people need to give me one or two lines about their research and I create a question around it. If they can answer it, they can play the game to win a shirt. This shows them that we belong to the chromatin community and they often feel more encouraged to talk about a given experiment or planned project.

Is there anything you always wanted to try out at a conference but didn’t do yet?

YES! In a perfect world, I would want to sit in a tweed jacket in my very British armchair, a boiling tea kettle next to me…people can sit down in my little chromatin tea room called “The Nucleosome” and have a relaxed chat around gene regulation and epigenetics with me, or do some networking with others.


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7 tips to successfully deliver wet-lab-based training courses

Are you planning a wet-lab-based training course but don’t know where to start? There are so many things that could go wrong! After 6 years as a training lab manager at EMBL,  I have seen it all. Here are some tips that could save you time, nerves and wasted lab consumables.

Our final meeting with the organisers and trainers of the EMBO Practical Course: Humanized Mice, to go over the finishing touches of the lab practicals. PHOTO: EMBL Events

1. Identify your main contacts

Whilst the course organisers are the experts with regards to subject and course content, they are often very busy and trying to get hold of them can be a difficult task. Most of the time they will appoint an experienced colleague in their lab to help with the more practical and logistical aspects of organising the course. These people are the key players for my job – it is generally with them that I organise the practical set-up, because they know exactly what is needed, and when.

2. Timing is everything

Trainers are always surprised by how much longer people need in the lab for things they are doing for the first time. From my experience participants need twice as long in the lab as people who do the experiment regularly. So have this in mind when planning the schedule for a course. If possible, perform dry runs to get a better feeling of how long some experiments really take, and then double that time.

3. Back up, Back up, Back up

Not every experiment that we run during a course will be successful, but it is not the end of the world if you have prepared some back-up samples. The course days are already long enough – nobody wants to miss dinner to repeat a failed experiment, and troubleshooting is also a valuable lesson for the participants.

4. Everything clear?

Giving clear, coherent instructions is one of those things that sounds easy to do but in real life can actually be more complex, especially in a course setting. Some trainers don´t feel comfortable raising their voices to get everyone’s attention, meaning they have to repeat every single thing over and over again, which can cost valuable time.

5. Having good relationships to the main lab

You can plan a practical down to the smallest detail, but someone might still forget to tell you things like, “Oh, your incubator is actually too small to fit the instrument in there!” or “Oops! All my cells died over the weekend!”

In these situations it is key to have a good knowledge about who is doing what in the main lab and is willing and able to help out. Luckily my cheerful personality and baking skills have saved the one or other practical!

6. P p p poker face, p p poker face

As much as I love to have everything planned ahead of time, often this is not the reality when planning courses. Instructors often travel from abroad, and by the time they have arrived on-site, there are so many things that could go wrong. I refer to the first couple of days before the course starts as the “headless chicken mode”. But thanks to the experience and skill of our trainers, we always manage to overcome any difficulties that arise and are able to deliver our courses professionally – and the participants aren’t affected in the slightest!

7. Always be prepared for the unexpected

“It was working fine until this morning!”- This is one of the sentences nobody wants to hear during a course, but that is just how it is in the lab sometimes, and the training lab is no exception. You need to be a flexible thinker and be able to find a solution so the course can go on. Find a replacement instrument, shift the schedule around until the problem is solved. If there is no quick fix come up with another activity and cover the topic theoretically.

But to be honest in these cases I am so happy that I am doing this job at EMBL— because the EMBL people never let you down.

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Best Poster Awards – Target Validation Using Genomics and Informatics

Meet Giovanni Spirito and Borja Gomez Ramos – the two poster prize winners at the recent EMBL – Wellcome Genome Campus Conference: Target Validation Using Genomics and Informatics (8 – 10 Dec 2019).

Identification and prioritization of candidate causal genomic variations from individuals affected by ASD

PHOTO: Giovanni Spirito

Authors: Giovanni Spirito (1), Diego Vozzi (2), Martina Servetti (3), Margherita Lerone (3), Maria Teresa Divizia (3), Giulia Rosti (3), Livia Pisciotta (4), Lino Nobili (4), Irene Serio (4), Stefano Gustincich (2), Remo Sanges (1)

Next generation sequencing (NGS) technologies enabled the extensive study of the genomics underlying human diseases. Namely whole exome sequencing (WES) represents a cost-efficient method which can lead to the detection of multiple classes of genomic variants and the discovery of novel disease-associated genes. One of the drawbacks of this approach however, is the large number of genomic variants detected in each analysis. Automated variant prioritization strategies are therefore required. This is particularly important in the case of complex disease such as ASD, whose genetic etiology is still poorly understood. To this aim we built a custom computational framework capable, from raw WES data, to automatically detect four classes of genomic variants (SNPs, indels, copy number variants and short tandem repeat variants) and prioritize them in regards to their relevance to a specific phenotype. We tested this framework on a selection of 29 trios including probands affected by severe and undiagnosed rare phenotypes and a small cohort of 10 trios all featuring healthy parents and one offspring affected by autism spectrum disorder (ASD). We were able to successfully detect rare and de novo high penetrance variants which have been validated and confirmed as causative among the undiagnosed probands. In the specific case of the ASD cohort we could highlight several genes which are not implicated in autism susceptibility, but nevertheless whose connections to genes relevant for ASD could suggest a possible involvement in the phenotype. Furthermore, our approach enabled us to detect several instances characterized by the presence of multiple candidate variants within genes belonging to the same canonical pathway in one proband. Our workflow allows to detect and prioritize multiple classes of genomic variants in order to both highlight rare high penetrance disease-causative mutation, and possibly reconstruct the genomics at the basis of complex ASD phenotypes.

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(1) SISSA, Italy, (2) IIT, Italy, (3) Gaslini Institute, Italy, (4) University of Genova, Italy


Omics data integration for the identification of cell-type-specific gene regulatory networks and regulatory variants in Parkinson’s disease

PHOTO: Borja Gomez Ramos

Authors: Borja Gomez Ramos (1,2), Jochen Ohnmacht (1,2), Nikola de Lange (2), Aurélien Ginolhac (1), Aleksandar Rakovic (5), Christine Klein (5), Roland Krause (2) , Marcel H. Schulz (6), Thomas Sauter (1), Rejko Krüger (2,3,4) and Lasse Sinkkonen (1)

Genome-Wide Association Studies (GWAS) have identified many variants associated with different diseases. However, it is still a challenge to make sense of this data as the majority of genetic variants are located in non-coding regions, complicating the understanding of their functionality. In the last few years, it has been found that non-coding genetic variants concentrate in regulatory regions in the genome, which are cell type and cell-stage specific. In this project, we seek to identify functional Parkinson’s disease GWAS non-coding genetic variants that could make carriers more prone to developing PD. To do so, we are using induced pluripotent stem cell (iPSC) technology to differentiate somatic cells into midbrain dopaminergic (mDA) neurons, astrocytes and microglia. Assessing their chromatin accessibility, active chromatin regions and transcriptome, we can identify crucial regulatory regions in the genome, key transcription factors and derive the gene regulatory networks for the three different cell types. Then, we will map the non-coding genetic variants to the different regulatory regions and predict their effect in silico for the subsequent validation in vitro. This innovative approach will also identify novel factors controlling cell fate and cell identity.

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(1) Life Sciences Research Unit, University of Luxembourg, Luxembourg, (2) Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Luxembourg, (3) Centre Hospitalier de Luxembourg (CHL), Luxembourg, (4) Luxembourg Institute of Health (LIH), Luxembourg, (5) Institute of Neurogenetics, University of Lübeck, Germany, (6) Institute for Cardiovascular Regeneration, Uniklinikum and Goethe University Frankfurt, Germany


Working on your own conference poster? Then check out 10 tips to create a scientific poster people want to stop by.

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