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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Meet the Trainer – Imre Gaspar

Meet Dr. Imre Gaspar, Senior Research Assistant in the Kikuë Tachibana Group at the Institute of Molecular Biotechnology in Vienna, Austria, which focuses on understanding how chromatin is spatially reorganised in totipotent cells.

What is your research focus and why did you choose to become a scientist?

I’m interested in the central dogma, that is how gene expression is regulated on the transcriptional and post-transcriptional levels and how these regulations allow development of an organism.

I became a scientist because I always fancied solving riddles – and as a scientist you get to work on solving the ultimate riddle that interests us, humans.

Where do you see this field heading in the future?

Right now, there is a boom of high-throughput and omics techniques in studying gene expression allowing us to create predictive quantitative models of regulatory networks, which will allow us to get mechanistic understanding of the processes underlying development, homeostasis and pathogenesis. Microscopy analysis is already essential for the latter and is also gaining importance also in the omics studies with the advent of high-throughput hybridisation techniques.

What is your number one tip for people looking for scientific training?

Being a microscopist, it was absolutely essential for my career to receive training in state-of-the-art imaging and image analysis technologies. Courses are important, of course, but I find that the best source of training a scientist can receive is core facilities, internal trainings, and of course close colleagues in the lab.

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

I have a degree in medicine, so I probably would have become a medical software developer – that profession is closest to the work of a scientist and having a background in medicine would allow me to contribute to the development of medical instrumentation.

You are organising the EMBO Practical Course ”FISHing for RNAs: Classical to Single Molecule Approaches” (15 – 20 March 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

We are at the onset of quantitative analysis in biology: many labs have already implemented corresponding work-flows, but this principle should be spread widely, especially in the fields working on the understanding of gene expression. I expect that the single molecule techniques we will cover during the course will serve as mind-changers to help people embrace the concept of quantitative biology.

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Meet the Trainer – Anna Kreshuk

PHOTO: EMBL/Marietta Schupp

Meet Dr. Anna Kreshuk, a group leader in the EMBL Cell Biology and Biophysics unit, whose group uses machine learning to develop automated methods to help biologists speed up image analysis. Anna joined EMBL in 2018 and has since been very active in building up training opportunities in her research field.

What is your research focus and why did you choose to become a scientist?

My research is concerned with developing new machine learning-based methods of the analysis of biological images. I enjoy doing science, both for the thrill of finding new things and the joy of seeing others do that in their domain with the help of our tools.

Where do you see this field heading in the future?

I hope to see most of the routine image analysis automated in the future. This will hopefully raise new research questions in biology which can only be answered by imaging at scale, creating, in its turn, more exciting research questions for us.

How has training influenced your career?

We develop software for end users without computational expertise, who want to solve biological problems we don’t quite understand. Participating in training has provided a lot of insight to the user side of things, brought new collaborations and even new research directions for me and for my group.

What is your number one tip for people looking for scientific training?

A one-week course can be a great start, however, it’s important to find out how you can get support with the new technology in your everyday work. Try to stay in contact with your course buddies, but also look for online communities. For image analysis, for example, there is a great forum connecting all the popular tools.

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

My 7-year-old recently asked: “you say I can become anything I want to be, but then why didn’t you become an astronaut?”. Seriously though, I’d probably be a programmer, I love automating things.

You are organising the EMBL Course: Deep Learning for Image Analysis (20 – 24 January 2020). What is the greatest benefit of the course for the scientific community and what could the techniques in this course be used for in the bigger picture?

Deep learning has brought an enormous advance in computer vision. We can now analyse microscopy images in ways no one thought possible just 10 years ago. While the technology is getting more accessible every year, it’s still difficult even for computationally savvy biologists to apply state-of-the-art methods to their image analysis problems. This is exactly the gap we intend to close.

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Meet the Trainer – Katharina Danielski

Meet Katharina Danielski, Field Application Scientist at 10x Genomics, who is an organiser and trainer at the EMBL Course: Immune Profiling of Single Cells (10 – 13 February 2020).

 

 

 

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

It provides researchers with an overview of what is currently possible when studying the immune system at the single-cell level. There are so many new technologies and methods available these days that scientists are overwhelmed with keeping track of everything new. The 10x Genomics Single-Cell Immune Profiling solution allows you to study a broad range of aspects all derived from the same single cell: sequence information of paired full-length T cell or B cell receptor transcripts; gene expression profile; cell surface protein markers; antigen specificity. Linking all these pieces of information back to the same cell is opening a lot of new ways to study the adaptive immune response that were just not possible before.

Are the methods used in this course unusual or new?

The ability to study single cells to the extent as it is currently possible with various assays on the market is still very recent. We are only beginning to scratch the surface of the biological information that will be uncovered in the coming years thanks to the methods discussed in this course, among others.

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

I enjoy teaching at EMBL because of the high level of organisation that the EMBL team displays. The EMBL Heidelberg Campus is also a particularly beautiful location situated on top of a hill surrounded by forests. But most importantly: the food in the canteen is legen- wait for it -dary.

What is your number one tip related to the course?

Don’t be shy. The trainers are more than happy to answer your questions and discuss your projects and  experiments…but skip breakfast so you can fill up on lunch at the EMBL Canteen. You will thank me later.

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

I don’t think any single discovery on its own could be labeled as “the most crucial”. Science in the past 100 years has made so many giant leaps for mankind.

Where is science heading in your opinion?

Studying gene expression of (single) cells spatially resolved within their morphological context of an intact tissue section.

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Meet the Trainer – Anders Ståhlberg

Meet Dr. Anders Ståhlberg, Associate Professor at the University of Gothenburg and  Sahlgrenska University Hospital in Sweden, and organiser of the EMBO Practical Course: Single-Cell Omics (12 – 18 May 2019) and EMBL Course: “Liquid Biopsies” (23 – 28 September 2019).

Anders’ research focuses on basic tumour biology and cancer diagnostics.

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

Liquid biopsy analysis is an emerging tool in biological/medical research as well as in clinical diagnostics. However, most analyses require ultrasensitive methods. In this course we cover both theoretical aspects and practical consideration that need to be addressed to utilise the potential of liquid biopsy analysis, and use both state-of-art techniques and novel approaches.

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

The applied techniques include ultrasensitive analysis of DNA, proteins and single-cells. These techniques can be applied to a wide range of applications in any type of liquid biopsy. In addition, these techniques can be used on any type of challenging sample types. Application areas include cancer, immunology, prenatal testing, forensics, evolution studies, drug screening, pathogen detection and beyond.

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

The superb facilities, including everything from course arrangement to the research lab. However, the best part of EMBL courses is the dynamic interactions between teachers, tutors, staff and all students. It is a perfect environment to network and discuss science.

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

The course dinners are very enjoyable and may end in unexpected but fun ways.

What challenges is your research field facing?

Translating basic research into clinical use.

Where is science heading in your opinion?

The amount of generated data will increase dramatically with all available high-throughput methods. One major challenge is to translate this data into useful information.

What was your first ever job?

I got my first job when I was 15 years old in basic industry, making valves.

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

A teacher or farmer.

What is the greatest risk you’ve ever taken?

In science, saying no to academically rewarding positions and instead following my research interest with an unsure future.

What is your favourite book?

I cannot resist a good fantasy book.

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