Meet the Trainer – Toby Hodges

PHOTO: Toby Hodges

Today we meet Toby Hodges from EMBL Heidelberg, who is an organiser and trainer at the upcoming EMBL Course: Computing Skills for Reproducible Research: Software Carpentry (16 – 18 October 2019). At EMBL, Toby supports EMBL’s bioinformaticians, providing training, advice, community building events and resources for computational science.

What is the greatest benefit of the course for the scientific community?

Computational research skills have never been in greater demand, particularly in the biological sciences. To meet this demand, many researchers must learn programming, command line computing, and other techniques required for data analysis. This Software Carpentry course provides a solid foundation for these skills, teaching researchers good practices in software and analysis pipeline development. The skills and experience that researchers gain by participating in the course will promote high-quality, efficient, and reproducible computational science.

What could the techniques in this course be used for in the bigger picture?

Almost anything! Command line computing, programming, and the other skills taught in the course are becoming vital in most areas of biology but are also widely applicable in a lot of other sectors and career paths – web design, journalism, politics, you name it! Of course, we hope that every researcher who attends our workshops will go on to a long and wildly successful research career but, should they choose to go in a different direction, we’re sure that the skills taught here will still prove beneficial.

Are the methods used in this course unusual or new?

New? Certainly not – most of the tools and techniques taught in our course have existed for many years already. What’s unusual, though, is for biologists and bioinformaticians to have the understanding of good practices in software development and workflow management that the workshop provides. Unfortunately, there’s still a lot of poorly-documented and poorly-written scientific software out there. Once they’ve attended our workshop, researchers will be better able to ensure that the programs and pipelines that they create are reproducible and reusable.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

It’s helpful for us to teach in a relatively informal environment. We find that, when course participants are relaxed, it creates a positive environment in which they can learn. We’re also privileged to have access to such great teaching facilities and to have excellent support from our colleagues in EMBL’s Course and Conference Office, who make it very easy for us to teach these courses.

What is your number one tip related to the course?

Make the most of it, both as an opportunity to learn from the trainers and as a chance to develop your network. The coffee and lunch breaks are a great chance to get to know your fellow course-mates, to share ideas and experiences, and to learn more about everyone else’s journey to this point.

What challenges is your research field facing?

It’s becoming increasingly important to think about how we manage our research data. The volume of data produced in a typical experiment has become enormous in recent years and we’re scrambling to catch up. It’s vital that our research data is well-annotated and retrievable so that others can re-use it and reproduce our results in the future, but ensuring this can be challenging. The other major challenge to my work is the sheer volume of different research techniques, tools, and data formats being used in modern biology. Bioinformatics has such a diverse ecosystem of tools and file formats, which is developing at a breathtaking pace. It can be difficult to stay up-to-date.

Where is science heading in your opinion?

The future of biological research will increasingly involve the integration of many different types and formats of data into a single experiment or study. We already see this in multi-omics studies and the increasing combination of imaging and single-cell sequencing techniques and I expect the trend to continue towards these integrated approaches.

What was your first ever job?

Stacking shelves in a supermarket.

If you were a superhero what power would you have?

If I could choose: the ability to never make a typo. If I don’t get to choose then, sadly, it would probably be deafeningly loud voice.

 What is your bucket list for the next 12 months?

After a very hectic few years, my main target for 2019 is to get better at saying “no” to things.

What is your favourite recipe?

Michael Chu’s Classic Tiramisu: http://www.cookingforengineers.com/recipe/60/The-Classic-Tiramisu-original-recipe

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Meet the Trainer – José Eduardo González-Pastor

meet the trainer - eduardo gonzalezJosé Eduardo González-Pastor – one of the main organisers at the upcoming EMBO Practical Course: Microbial Metagenomics: A 3600 Approach (12 – 19 June 2019) – conducts his research on the mechanisms of adaptation of microorganisms to extreme conditions using metagenomic and metatranscriptomic approaches at the Center of Astrobiology (CSIC-INTA) in Madrid, Spain.

What is the greatest benefit of the course for the scientific community?

One of the greatest difficulties in the study of microbial communities is that a large percentage of the environmental microorganisms can not be cultivated. Numerous tools, called “omics” have been developed, such as metagenomics, metatranscriptomics and metaproteomics, which allow access and study of all microorganisms in these communities. In this course, we explain most of these methodologies from theory and practice, and how to use them to properly design experiments to answer certain scientific questions related to microbial communities.

What could the techniques in this course be used for in the bigger picture?

The “omics” techniques allow us to better understand the functioning of microbial communities in their natural environment and not exclusively in laboratory conditions. In addition, one of the techniques, namely functional metagenomics, is very useful for recovering enzymes of interest in biotechnology from the microorganisms of the environment.

Are the methods used in this course unusual or new?

In the course we will explain some recent methods in functional metagenomics, such as the screening of metagenomic libraries using microfluidics techniques.

In comparison to other training environments, what do you enjoy most about teaching at EMBL?

The support from the EMBL Course and Conference team in the organisation of the course is impressive. All the logistics and other matters such as the preparation of the laboratory are handled very professionally by them. We, as trainers and organisers, only need to dedicate ourselves to coordinating the scientific part, and that leaves us time to interact with the students.

What challenges is your research field facing?

The methods of massive sequencing of DNA are generating a lot of information, but we still do not understand the function of a very high percentage of genes, which encode hypothetical or unknown proteins. Even for Escherichia coli, the best studied of all organisms, half of all the proteins encoded in its genome, around 2,000, have never been experimentally characterised. Thus, we need the combination of new and classic methods to be able to understand the molecular functioning of the organisms.

What, in your opinion, is the most crucial scientific discovery of the past 100 years?

The discovery of the structure of DNA.

What is the most interesting paper you’ve read in the past year?

GABA-modulating bacteria of the human gut microbiota. Nat Microbiol. 2019 Mar;4(3):396-403. doi: 10.1038/s41564-018-0307-3. Strandwitz P, Kim KH, Terekhova D, Liu JK, Sharma A, Levering J, McDonald D, Dietrich D, Ramadhar TR, Lekbua A, Mroue N, Liston C, Stewart EJ, Dubin MJ, Zengler K, Knight R, Gilbert JA, Clardy J, Lewis K.

Human microbiota and depression!! Microorganisms are much more relevant than we thought.

Where is science heading in your opinion?

Applied research is being favoured more than basic research, and it is a serious mistake, since much of the advances in applied science have their origin in basic research. The scientific community faces very complicated challenges in applied science without having solved many basic questions about the functioning of organisms. How can we undertake the search for new tools to fight pathogenic microorganisms if we still do not know the function of a large majority of their proteins?

What was your first ever job?

Postdoctoral position at Harvard University, Department of Molecular and Cellular Biology. Cambridge, MA, USA.

If you weren’t a scientist, what would you be?

Architect, musician or chef, in this order.

What is the strangest or funniest thing that has ever happened in a course?

It was not so funny but strange. In the first course that I collaborated as a trainer and speaker (not as an organiser), “Metagenomics: From Bench to Data Analysis”, the two EMBO organisers had to leave in the middle of the course for personal and urgent reasons, and suddenly one of the course assistants gave me the keys of the rooms and I had to take responsibility for organising the course until the end. Possibly I did not do it badly, since the EMBO organisers decided to invite me to be also an organiser of the following editions of this course, which is now “Metagenomics: a 360º Approach”.

If you were a superhero what power would you have?

To be able to access the minds of others.

What is your bucket list for the next 12 months?

Decrease administrative tasks and complete the writing of several pending articles.

What holiday tip can you give people – e.g. a place / restaurant / attraction you have visited in the world that people should definitely make the effort to see?

To visit the Antarctic.

What is the greatest risk you’ve ever taken?

Crossing the Drake Passage (Sea of Hoces) by ship to go from Punta Arenas (Chile) to the Antarctic.

What is your favourite book?

The Little Chronicle of Anna Magdalena Bach, by Esther Meynell

What is your favourite recipe? Please provide details!

Black rice with seafood (paella negra de marisco, in Spanish). Rice is cooked in a sauce with tomato, red and green peppers and onions, then it is added a broth made with fish, seafood remains and squid ink. During cooking, shrimps, clams, squids and green beans are added.

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Training in numbers

For those of us who like data, end of year statistics are like the holidays all over again. It’s a few days combining the external training data from all six EMBL sites, then playing with excel sheets and pivot tables galore. The point of it all? We want to know how many scientists we reach each year, and our goal is to train as many scientists as possible – after all, sharing is caring, and training is one of EMBL’s core missions.

External training activities at EMBL focus largely on the events in the Course and Conference Programme , which saw 7,148 people come through EMBL’s doors in 2018, around 500 more than in 2017. We had 59 courses and 26 conferences across our sites in Heidelberg, Hinxton, Hamburg and Grenoble. For us here in Heidelberg, there was never a dull moment, from the intimate meetings with 50 participants, to the conferences that filled the Klaus Tschira Auditorium to capacity or the course participants chatting away during the coffee breaks. In addition, 345 delegates received financial assistance to attend one of our events, thanks to the EMBL Corporate Partnership Programme and EMBO, as well as Boehringer Ingelheim Fonds who provided support for various practical courses.

EMBL’s external training activities also comprise online training in bioinformatics and wet lab techniques, where we reached almost 500,000 users – and this doesn’t even count all the YouTube views. On- and off-site training activities carried out by EMBL faculty via lectures, workshops, conference exhibitions, etc are where we reach the most people. In total, EMBL staff reached more than 75,000 people – equal to about ½ the population of Heidelberg! The EMBL Scientific Visitor Programme, which allows scientists to come to EMBL through internships or collaborate on specific research projects had 688 students take part from all around the world.

As you can see, 2018 was a very busy year for all of us involved in external training. Whether it be group leaders, scientific organisers or teams of event organisers, it takes a lot of people to deliver the extensive and high quality training that EMBL has to offer –  so we would like to give a big THANKS to everyone involved!

 

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Meet the Trainer – Ashley Sanders

In spirit of the International Day of Women and Girls in Science (11 February), we are proud to launch our “Meet the Trainer” Series, in which we will profile some of the amazing trainers from the EMBL Course Programme. We begin with Dr. Ashley D. Sanders, a distinguished scientist in the Genome Biology Unit of EMBL whose research focuses on how single-cell genomes change over time and how this impacts cell behavior.

Ashley will be training at the upcoming EMBO Practical Course: Single-Cell Omics (12 – 18 May 2019) and we asked her to give us some insights and tips for the course, as well as answer some not so scientific questions.

What is the greatest benefit of the course for the scientific community?

Without a doubt, single-cell measurements have emerged as the most direct method for deconvoluting complex and heterogeneous samples, and for exploring how subpopulations of cells respond to experimental manipulations. This course will allow participants to learn some of the most cutting-edge technologies and gain valuable hands-on experience from leading experts in the field. I hope this will help inspire new research, discoveries and collaborations.

What could the techniques in this course be used for in the bigger picture?

New technology equips us with new tools to explore long-standing questions in biology. Emergent single-cell omics methods are now providing us with the chance to ask how individual cells differ in terms of their DNA mutational profiles, epigenomic states and transcriptional outputs – enabling us to explore dynamic cellular relationships through a new lens. In unravelling these relationships we will better understand how diversity is established and maintained in healthy human tissues, and how aberrations in these processes can lead to disease.

Are the methods used in this course unusual or new?

The course will highlight some of the newest and most exciting methods in genomic research, including single cell bisulfite sequencing, single-cell RNA-seq and Strand-seq. Strand-seq is a novel single-cell and strand-specific sequencing method and this is the first time it will be offered in a course format.

 What is your number one tip related to the course?

Engage. Take time to interact with the other participants and the trainers. This course offers a unique opportunity to meet your colleagues in the field of single-cell biology, which can lead to new relationships and collaborations.

What challenges is your research field facing?

Single-cell genomics is expensive, noisy and complex. We need to bring down the cost of production to increase throughput and access more cells. We need to improve benchtop protocols to generate higher quality data from each cell we invest in. And we need smarter and faster bioinformatics that extract meaningful signal and integrate data layers across cells and experiments.

Where is science heading in your opinion?

We are in a single-cell omics era. Novel approaches are now available to untangle complex biological systems through multi-layered and complementary data types. By designing smart experiments that integrate across these layers, I believe we are positioned to unravel how homeostatic multicellular tissues are generated and maintained. In understanding these nuanced and cooperative inter-cell relationships, we will be in a position to deliver more holistic cell-based health care. This may involve selectively targeting rogue cells that disrupt our systems or producing functional regenerative tissues for transplants.

What was your first ever job?

Selling coffee through the Tim Hortons drive-thru in Toronto, Canada

If you weren’t a scientist, what would you be?

Yoga instructor

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Meet the Team – The EMBL Event Survival Kit

The external training programme runs close to 30 conferences and over 60 courses per year, as well as running the EMBL visitor programme. Serving so many scientists mean there are a few things we need to help get us through the year!

Head of External Scientic Training & Head of Course and Conference Office
WHISKEY – To calm the nerves

Jürgen DekaGeoffrey Barnett
Jürgen & Geoff

A blend of German intensity and British stoutness, the Head of External Scientic Training (Jürgen Deka) and the Head of the Course and Conference Office (Geoff Barnett) perfectly complement each other with their dignified and slightly nutty characteristics. With a subtle malty aroma, they are a balanced mix of dryness and spice. Best enjoyed diluted and in small doses, this smooth duo ensures that the external training team consistently performs as a top notch, blended team.

External Scientific Courses & Visitor Programme
VITAMINS – To optimise performance


Yvonne, Elisabeth & Claudia

These essential minerals are vital to keeping our external training programme running and healthy. The 100% natural, maximum-strength team work well together to produce an optimised result, with all carrying out their diverse biochemical functions. Fine to consume on a daily basis, however be sure to do so in small amounts to prevent toxic reactions. They are a convenient cure all for all training related problems, with proven premium-quality side-effects.

Courses Team
CHOCOLATE – To keep up the energy levels


Maryann, Christina & Maria

Chocolate doesn’t ask silly questions, chocolate understands. It is always there when you need it. The Courses team are the quality chocolate production line when it comes to running great scientific courses. Rich and satisfying, this delightfully sweet team owes its success to the relentless and uncompromising pursuit of excellence, constantly aiming to please. Although at times bitter sweet, it is easy to become addicted to these premium beings – you are guaranteed to keep coming back for more!

Conferences Team
COFFEE – To stay awake after the conference parties


Tim, Nathalie, Lisa, Lea, Inna & George

The unmistakable aroma of this fragrant team is what makes the conference team unique. Carefully selected, they are roasted to perfection in order to keep you going from conference registration to the closing remarks. According to chemistry, coffee is a solution, and that is certainly true in the case of this earthy yet spicy group. Although there may be some fake, instant coffees out there who are intent on taking shortcuts, at EMBL we have the real thing, and guarantee that we have created the perfect brew for a successful conference.

Marketing Team
CHAMPAGNE – Because who needs an excuse to celebrate?


Julie, Nicola, Krasimira, Carolina & Assol

Focused and bold, the marketing crew make up a very strong team with a truly distinct sparkle of genuine creativity and freshness. Dazzling character that slowly develops along with the organisation of an event, embarking on the endeavours of analysing, proofing, advertising, as well as the subtle capturing of sponsors. Quite youthful, bubbling a myriad number of new and innovative ideas.

Administration
CAKE – To bring some sweetness to the team


Anna & Kathy

The perfect accompaniment to a hard day in the office. Perfect in design, bursting with a broad mix of flavours and characteristics, there is an option for everyone depending on their requirements. Often crisp on the outside but fluffy in the middle, these angelic cakes are devilishly good at what they do. Everyone has their favourite – whether zesty or wholesome, this perfectly presented, irresistible duo help everyone make it through their daily grind!

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