We’ve proved it, biologists can also program

“Like punning, programming is a play on words.” Alan J. Perlis.

You don’t have to be a programmer to have programming skills. Writing code is an essential part of being a programmer (duh!), but is also a vital component of being a scientific developer, software developer or computer scientist. You can utilise computer programs to automate tedious and repetitive tasks, extract results from experimental data, apply models to solve your research questions or purely have fun with your own projects.

Today is Programmers’ Day (yay!🥳) and we want to recognise all those who submerge themselves in the deepest mysteries of code (especially their own) and aim to automate the future.

If you’re looking to start venturing into the programming world or embark on your next project, get some inspiration from some scientists who are helping out at our EMBL Events’ courses.

Florian Huber PHOTO: Marietta Schupp/EMBL

“What do I love about programming? It allows me to go from zero to one: gaining new biological insights from data.” Florian Huber (Postdoctoral Fellow, at the Typas Group in EMBL Heidelberg and the Beltrao Group at EMBL–EBI in Hinxton).

 

 

 

 

Ullrich Köthe PHOTO: Ullrich Köthe

“Automated image analysis has always been an interesting and fun field of research, but thanks to the deep learning revolution and the wide availability of wonderful neural network libraries, we can now actually solve hard practical problems.” Ullrich Köthe (Group Leader in the Visual Learning Lab Heidelberg).

 

 

Valentyna Zinchenko PHOTO: Carolina Cuadras/EMBL

“Programming skills allow you to automate the routineparts of your job and focus more on the exciting ones. At some moment you just have so much data, that you would not want to process it manually. You would not wash your clothes by hand if you have a washing machine, would you? Then why analyzing your data manually, when you can have it done by a machine as well?” Valentyna Zinchenko (Predoctoral Fellow in the Kreshuk Group).

 

Adrian Wolny PHOTO: Carolina Cuadras/EMBL

“Whenever I build something, be it a new machine learning model or my pet project, I always try to make it easy to understand and generic enough so that other people could use it in their work. I try to open source my projects whenever I can and contribute back to the community. There is nothing more rewarding than seeing your little piece of software used by others to find answers to their own research questions.” Adrian Wolny (Visiting Researcher at EMBL and PhD candidate at Heidelberg University).

 

Pavel Baranov PHOTO: Pavel Baranov

“The relationship between computer science and modern biology is akin to that between mathematics and physics.” Pavel Baranov (Professor of Biomolecular Informatics, University College Cork, Ireland)

 

 

 

 

It’s no secret that managing biological data efficiently can be overwhelming and feel impossible. If you’re a biologist who’s interested in learning how to process, analyse, organise and interpret your almost innumerable data sets – preferably with the most suitable and state-of-the-art techniques and tools out there – EMBL Events has got you covered.

EMBL Course: Deep Learning for Image Analysis, Apply by 20 September 2019

EMBL Course: Exploratory Analysis of Biological Data: Data Carpentry, Apply by 5 November 2019

EMBL Course: Analysis and Integration of Transcriptome and Proteome Data, Apply by 10 November 2019

EMBL Course: Immune Profiling of Single Cells, Apply by 10 November 2019

EMBO Practical Course: Microbial Metagenomics: A 360º Approach, Apply by 27 January 2020

EMBO Practical Course: Measuring Translational Dynamics by Ribosome Profiling, Apply by 9 February 2020

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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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A big “Thank You” to our supporters

We would like to thank all our supporters of the 2018 EMBL Course and Conference Programme. With their help we were able to provide top-class training and keep the registration fees as low as possible allowing more people to profit from these opportunities. 86 companies sponsored a total of 25 events in Heidelberg and here is what some of them had to say about their experience:

“The audience comprised a very good mix of members from academic institutions and industry. We appreciated the rich interactions during the conference and friendly social events. Of course we were pleased to see a high interest in our activities and products and are confident we will build interesting collaborations in the future thanks to this event.” (Ectica Technologies)

“The conference program gathered a broad panel of microfluidic experts that presented the latest scientific discoveries in the field. The exhibition setting allowed me to easily interact with a broad range of participants and establish new valuable connections.” (miniFAB)

“The pre-conference workshop was very well attended and supported by the organizers, the booth location and interaction were excellent. The product fit for our portfolio of organoid culture products and tools was excellent and the organization, as always, was great, which goes a long way to creating an open and collaborative atmosphere that benefits exhibition.” (STEMCELL Technologies)

“EMBL is one of Europe’s most prominent life science institutions and as such gathers numerous eminent researchers across Europe and around the world. EMBL also covers a wide scope across the life science research allowing to target specific users. Compared to other scientific conferences, we also appreciate the good price / performance ratio of EMBL events.” (Wako Chemicals)

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A team effort

Friday night the entire EMBL Events team came together in the Heidelberg old town for our annual social. It’s tough to organise an event for 65 people who spend their time organising events. Even agreeing a date is a mammoth task as they are usually busy working on an event….but somehow it seemed to work out. Our caterers ate their dinner, the transport team found their way to the venue, the events managers sat still and let someone else run the show and the finance team agreed to pay the bill. All good signs!

You only realise how many professions come together to produce the events programme here at EMBL’s Advanced Training Centre when you put everyone in the same room. Designers, marketing, AV, transport, catering, facility management, accountants, security and of course event planners to name a few…. and these are just the in-house services. Off campus we rely heavily on our amazing local suppliers – Heidelberg’s hoteliers and musicians, our printers, florists, bus and shuttle service drivers. Without all of them, the programme of 80+ events would not be possible and we are very thankful for the outstanding support they provide every year.

But now, after an enjoyable and relaxing evening, it’s back to work for all on an expansive 2019 program!

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