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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Fostering friendly collaborations across organisations

Guest blog post by Jürgen Deka, Head of External Scientific Training, EMBL

The International Day of Friendship (annually on 30th July) got me thinking about our friends in the scientific training field, and our collaborations with them which enable us all to deliver our high-level scientific conferences and courses.

It’s important to have a goal to work towards, and at EMBL Events we generally benchmark ourselves against Cold Spring Harbor Laboratory and Keystone Symposia in the US, and the Wellcome Genome Campus in the UK. A bit of healthy competition is good for the soul, and I think we all thrive on challenges! It allows all four of us to provide top-class training to benefit as many scientists as possible throughout the world, and in this sense we all have the same aim.

“Competition has been shown to be useful up to a certain point and no further, but cooperation, which is the thing we must strive for today, begins where competition leaves off.”    

Franklin D. Roosevelt

If you are looking to establish and foster friendly collaborations in scientific training, here are 6 tips that can help you achieve your goal:

  1. Keep in regular contact
  2. Align your goals with each other
  3. Be aware of what the other organisations are doing and talk to them openly so you can adapt your plans accordingly
  4. Don’t arrange meetings with the same audiences too close together. If people are going to attend both meetings – either as speakers, participants or sponsors – there needs to be some space in between
  5. Find ways to work together in order to highlight and complement your strengths
  6. Learn from each other, but don’t try to be like the others – work on developing your own strengths

Here’s how we work with our counterparts to allow us all to offer the best science possible worldwide:

  • Cold Spring Harbor Laboratory: With the Cold Spring Harbor Laboratory we have very close ties. We alternate one of our most popular conferences with our friends at CSHL, the EMBO Workshop ‘Protein Synthesis and Translational Control’. We align our programme plans in order to provide added value for our scientific community. Discussion and exchange between the programme heads and other members of staff takes place on a regular basis.
  • Keystone Symposia: As with the other research institutes, EMBL’s collaboration with Keystone Symposia is a long-standing one. We exchange our thoughts and ideas and align our conference programmes once per year. Our friends at Keystone Symposia have been particularly open and collaborative with regards to the alignment of their symposia taking place in Europe.
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Balancing training with family

Balancing work with family life can be difficult, and often the opportunities for parents to advance their careers are limited as a result. EMBL and EMBO are both working to make attending scientific events easier, with EMBL providing onsite childcare at their conferences and symposia in EMBL Heidelberg, and EMBO offering childcare grants to cover the costs of having a child looked after while one or both parents attend an EMBO funded course or conference.

To avoid any confusion between the two options, here is an overview of what you might be eligible for to help you get the most out of your career and your family.

At a glance

  EMBL onsite childcare EMBO childcare grant
Eligibility EMBL Conferences,  EMBO Workshops or  EMBO| EMBL Symposia taking place at the EMBL Advanced Training Centre Heidelberg, Germany. EMBO Courses, Workshops or EMBO| EMBL Symposia. The EMBL Course and Conference Office deals only with those events taking place at the EMBL Advanced Training Centre Heidelberg, Germany. Grants for other EMBO events should be applied for directly to the individual event organisers.
Who and where? Children are looked after on campus by our highly qualified kindergarten teachers in the EMBL Kinderhaus, Heidelberg, Germany. Childcare grants are available to offset child care costs incurred by participants or speakers of EMBO events. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, or travel costs for bringing the child to the city/town where the meeting is being held, etc.
Languages The two main languages of the teachers are German and English. N/A
Childcare times 8:30am – 5:50pm for the duration of the conference Grant applicable for costs incurred in relation to child care costs during the meeting.
Financial details A subsidised fee of €100 per child is payable by the conference participant A total of €1000 is available per meeting, with a general cap of €500 per person. This can be allocated based on need at the discretion of the organisers.
What’s provided? All necessary equipment such as meals, beds, toys and diapers are provided. Eligible costs include fees for a baby-sitter or child-care facility, travel costs for a care giver, or travel costs for bringing the child to the city/town where the meeting is being held, etc.
Who is eligible? One or both parents must be registered participants, organisers or speakers at the corresponding conference. The child must be between 3 months and 3 years of age. Childcare grants are available to anyone attending the event (speakers, organisers, trainers, participants etc.)
How to apply Registration for childcare must be made online 6 weeks before the start of the event by using the “register for childcare link” on the individual conference website. Applicants must indicate during the abstract or motivation letter submission process how much funding they would like to apply for, and what it will be used for. They should also indicate at what stage of their career they are.
Allocation process As childcare spaces are limited, registration will be on a first-come first-served basis. Your place can only be confirmed after payment of the registration fee. The selection is handled by the EMBL Course and Conference Office. The amount of money awarded for the childcare grant is dependent upon the number of applicants per event. The selection is handled by the organisers of the respective meetings.
Contact details childcare@embl.de or Tel.: +49 (0)6221 387 8797. Please contact the organisers of the individual event for more information.
Website EMBL Onsite Childcare

EMBL childcare testimonials

EMBO Childcare Grants

Press release – EMBO childcare grants now available

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BioMalPar’s most loyal friends

Meet Prof. Peter Preiser and Dr. Stefan Rahlfs, two of BioMalPar’s most loyal participants, who have not missed a conference since 2009 and 2010 respectively. They recount their experience from previous events of the series and share with us their expectations of the upcoming conference.

How has the conference developed over the years in your opinion and what makes you come back every year?

PP: The BioMalPar conference is unique in that it is one if not the only annual conference that focuses on the molecular and cellular aspects of the malaria parasite. It therefore has always represented an ideal meeting to catch up with the latest developments in the field. Due to its focus on giving PhD students a chance to present their work the meeting always had a “new” feel to it which I particularly appreciated.

SR: The conference has always drawn participants from all over the world, and presented interesting talks by both experienced and young researchers. However, getting to the conference venue used to be much more difficult and the early events took place in office rooms and a tent (it was pretty hot in there!). But things have changed significantly since then. Now there is a new parking garage, a new conference centre, which I like very much – light, modern, scientific.  The best part is the “helix” where you have to find your way walking on a base pair bridge .

PP: Clearly the conference has changed over time – this was partly due to the end of the EU funded BioMalPar programme and therefore the discontinuation of the PhD programme, but still it retained its focus on giving young researchers an opportunity to present their work. Today the meeting is a nice balance between young and more established researchers, which means there are the hot-off-the-press type presentations representing the work of a single researcher along with the more comprehensive research achieved through a multi-team effort.

SR: The quality of the talks remains impressive with a good mixture of topics. There is always a keynote lecture followed by short talks. Workshops and flash talks are now included and I have learned a lot about different people especially the ones receiving the Lifetime achievement award.

PP: The establishment of the Lifetime achievement award was something that I felt was particularly important as it provided many of the young researchers attending the meeting a perspective of the immense contributions the previous, slightly older generation had made to the field.

What’s the best memory you have of a BioMalPar conference?

PP: For me it has always been the relaxed attitude of the meeting and the opportunity to discuss science over a beer at the posters or outside (weather permitting) on a mild spring evening. Many fantastic ideas were generated through these discussions.

SR: The things that always stay in my mind are the fantastic venue, attractive program, nice age-mixture of people and the friendly atmosphere. I always go home with respect for others’ work but also with new ideas for my own research. At one of the BMP conferences I personally met Prof. Hagai Ginsburgh, and once he combined his stay in Germany with a trip to our Giessen-University for some days. This was very impressive and constructive at the same time.

In your opinion, what challenges is malaria research facing and how does coming to BioMalPar address these problems?

PP: I think the effort to control and eliminate malaria has made significant progress and we are now getting to a critical phase in the global effort. It is now important to ensure that efforts to control the disease are not slackened and that funders continue to support this important health initiative. From a research perspective we still have key challenges in terms of drug resistance and the lack of an efficient vaccine, not to mention the issue of P. vivax. It is particularly in these areas where BioMalPar can stimulate the right discussions and interactions that will eventually lead to significant benefits in controlling the disease.

SR: It is still a disease occurring in poor countries and resistance is always a problem. Although bed nets help a lot and a vaccine is available (which is not very effective, but the best mankind has been able to provide so far), research must go on. And in rural areas infrastructure for distribution of newly developed drugs or vaccines needs to be installed. For research there is a gap between industry (monetary research) and universities (basic research), which is due to their different settings.

Looking at the programme of this year’s conference, what do you think will be the highlight and what would you like to see in the next edition in 2020?

PP: This is hard to say as based on the titles there appear to be many new and exciting topics on the programme. I am quite intrigued about the work going on with the mosquito vector and possible ways a better understanding in this area may provide us with better tools for intervention. I am also excited about the use of stem cells to study malaria parasites, as this technology would significantly help me to address some of the questions I am interested in.

I think one of the key things that I would like to see develop more in the future is a better link between the basic research presented at the BioMalPar conference and how this could be utilised in a more clinically relevant context. For example, how does our understanding of malaria immunology help in developing a better vaccine or how do we use the vast amounts of genomic data more effectively for the discovery of new drugs, new vaccine targets or even better diagnostic markers. Some of this is already happening but a lot more can be done.

Prof. Preiser, you will present a short talk titled “Comparative mapping of Plasmodium proteomes provides new insights into erythrocyte remodelling”.  What can participants expect to learn from your talk?

I have always wondered about how the malaria parasites changes its host cell. In particular, I was intrigued about the apparent differences that different malaria parasite species have developed in modifying the same type of host cell. However, most of our knowledge on this is based on the study of a single parasite species P. falciparum. My lab has therefore tried to develop new approaches to study the differences the different plasmodium species have developed by using human, simian and rodent malaria parasite species and identify all the different proteins that the parasite exports into the host cell. This approach has given us some very surprising results that I will talk about during the meeting.

Dr. Rahlfs, you will present a poster titled “Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase: characterization of the Plasmodium vivax enzyme and inhibitor studies”.  Can you give us a short preview of your poster?

As a member of the “Becker-lab” in Giessen we are focusing on redox metabolism as drug target and on redox regulations in general and under stress. A number of gene knockouts of our group but also others mostly do not have big impact (due to redundancy), but the importance of the Glucose 6-phosphate dehydrogenase 6-phosphogluconolactonase (GluPho) in P. falciparum has been demonstrated by a lethal phenotype. Now we would like to expand this knowledge also on P. vivax. We cloned P. vivax glucose 6-phosphate dehydrogenase (PvG6PD), the C-terminal and NADPH-producing part of PvGluPho, recombinantly produced it in Escherichia coli, purified and characterised the enzyme. IC50 values of several compounds were determined on P. vivax G6PD, inhibitors that had been previously characterised on PfGluPho.

 

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Happy birthday VIZBI!

By guest blogger, Helena Jambor, PhD, TU Dresden, @helenajambor

10 years after it all started, VIZBI came back to its original stomping grounds, the ATC at EMBL in Heidelberg. As its name suggests, VIZBI “Visualizing Biological Data”  is a blend of several worlds. Of biology, with its long history in visualizations that goes back to Ancient Greek text books, and of art and scientific illustration.

Venn diagram of VIZBI disciplines: microscopy and EM data, transcriptomics and computer science. (Note: a 5-circle Venn cannot show all possible overlaps, which is fully intended here)

VIZBI is also inseparable from computer science and its tools to transform big data into human readable entities. And finally, VIZBI incorporates concepts of design and visual perception to make visualizations engaging and enlightening.

Highlighting spectacular biological images

At VIZBI 2010, microscopic images were omnipresent. Back then, I was embarking on my postdoc project, a large-scale microscopy screen of RNAs in cells. My memories tell me that this was the main focus of the conference. Indeed, a quick check of the 2010 program confirms that almost the entire community of light sheet microscopy and image processing were in attendance at the first ever event.

VIZBI 2019 continued to highlight spectacular biological images. A phenomenal augmented reality installation showed them in 3D, EM-tomography simulations by Peijun Zhang animated the 64-million atoms assembling into HIV particles, and Lucy Collinson shared the high numbers of high-resolution EM data collected at the Francis Crick Institute. This large amount of data is annotated with the help of amateurs, for example in their citizen science project at the Zooniverse “Etch a cell”.

Colourful confocal images or images of tissues also provided the inspiration to many works of illustrators on display that combined science and art, for example the double win of best poster and best art to a depiction of tubulin in a mitotic spindle by Beata Mierzwa @beatascienceart, a hugely talented artist and scientist (who also sells cool cytoskeleton-printed leggings and mini-brain organoid dresses).

Data visualization

At VIZBI 2019, visualizations of data – as opposed to images – gained a much more prominent spot. All keynote speakers were from the technology side. Hadley Wickham presented the history of ggplot2. Ggplot2 (and yes, there once was a ggplot1!) is the R universe for visualizing pretty much everything that comes in numbers and is now merged into the tidyverse. Being a visualization talk, all slides were themselves beautiful, I love the tidyverse playfully represented as stars of our universe! The second keynote was by Janet Iwasa who presented her animation work that heavily relies on 3D and computer graphics software used for animation films. Instead of earning her money in the film industry, she decided to put it to good use for biology. Janet first used her skills in her PhD project to visualize motor proteins “walking” along the cytoskeleton, and these days produces Oscar®-worthy movies showing biology, such as the origin of life or the life cycle of HIV. And everyone take note: all her films start as a storyboard on paper, which is what I teach as good practice for all visualization designs.

Making the invisible visible

The third keynote was by Moritz Stefaner, a data designer who is enticed by biological data but appalled by the time-scales in biological projects (too long!). Luckily, he hasn’t given up on us just yet, and keeps producing phenomenal visualizations. For example, showing absence and loss is notoriously hard, but Moritz found a beautiful way to make the invisible visible in his designs for “Where the wild bees are” with Ferris Jabr for Scientific American.

Making absence visible, a project by Keynote speaker Moritz Stefaner. Photo: H.Jambor

Moritz left us hungry for more when also showing his data-cuisine project, that visualizes data about food and turns food into data: the number of berries picked in Finland become a layered dessert, and common causes of death are encoded as praline fillings – you never know which one you’ll get! (Luckily this was with Belgium pralines, so all deaths are sweet.)

Feedback wanted!

Visualizations of data were in the spotlight of many other projects too. This is of course owed to the many possibilities of large-scale methods that swamped biology with data in recent years: RNAseq, inexpensive genome sequencing, mass-spec at fantastic scales, robotics driven biochemistry and medicine, image processing that turns images into insights by quantifying signals and so on. RNA sequencing, for example, fuelled Susan Clark’s project tracing methylations in cancer, Phillippe Collas’ ambitious endeavour to understand 3D genome architecture, and is empowered by Charlotte Soneson’s “iSEE” software to interactively analyse data from high throughput experiments and the project of Kirsten Bos tracing human pathogens back thousands of years by sequencing tiny dental samples. And of course, of the biggest data projects in biology is the ENSEMBL genome browser, which was officially released as pre-alpha version VIZBI (check it out: 2020.ensembl.org), the very approachable Andy Yates and his team are looking for feedback!

Technical Challenges

Visualizations of high-dimensional datasets are not without problems. The technical challenges were addressed by David Sehnal who showed computational infrastructure to visualize protein structures (MolStar). The mathematical problems of dimensionality reductions were a topic of Wolfgang Huber’s talk, and a tool to visualize, and thereby find(!), batch effects, “proBatch”, was presented in the flash talk by Jelena Čuklina (they welcome beta-testing by users!). Teaching science visualizations, I often see a great need to discuss ethical and practical aspects. Critically assessing limitations and challenges of scientific visualizations might be a topic to be expanded in future, when VIZBI enters its second decade. This should be coupled with visual perception research, after all, we are no longer limited by computational power, but rather by what our eyes and brains can comprehend (see Miller 1956).

Flash talks

“Data dancing” © Alex Diaz

Speaking of flash talks: the conference organisers did such a great job in highlighting every single one (!) of the posters by one-minute talks. I tremendously enjoyed them, admittedly in part because I have a short attention span. Among the talks and art was also “Data dancing” by Alex Diaz. He showed that art and beauty can also be found in statistics and numbers blossoming like flowers across the page. On that note: see you next year in San Francisco!

 

P.S. Many more highlights I was unable to cover here. Check https://vizbi.org/2019/ for all posters and slides of the flash talks, check #VIZBI on twitter and my public collection of participants twitter handles (https://twitter.com/helenajambor/lists/vizbi2019).

The VIZBI organising team – James Procter, George Luca Ruse, Seán O’Donoghue, Christian Stolte, photo: H.Jambor

 

 

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