Highlights from the 2019 Visualizing Biological Data (VIZBI) Workshop

Meeting report by EMBL event reporter Dagmara Kaczynska

In March I had the amazing opportunity to take part at the 10th Visualizing Biological Data (VIZBI) workshop as an EMBL event reporter. This year VIZBI lasted for 3 days and included various sessions: DNA, RNA, Proteins, Cellular Systems, Tissues & Organisms as well as Populations & Ecosystems. As it was my first VIZBI conference I had wondered how it is possible that one workshop contains such a diversity of topics. Who is the audience? Who are the speakers? Even if you missed the VIZBI workshop this year, let’s relive it together.

What is VIZBI?

To start uncovering VIZBI let’s first visit the website. It shows that VIZBI focuses mostly on how data is represented, not only what it presents. What’s more, we learn that the audience consists of a variety of crafts such as scientists, medical illustrators, graphic designers, artists and computer scientists. This multidisciplinarity is also visible in the program of the conference. Although most of the speakers are researchers, we can also expect talks from statisticians, computer scientists, animators and data visualization experts. This collaborative approach of VIZBI makes it possible to find common patterns and guidelines to make a good visualization of biological data. Most importantly, participants of the VIZBI conference believe that good visualization is the key to scientific communication.

While thinking about a visualization, think about data first

To begin with, let’s slice and dice the ‘biological data visualization’ concept by asking – what is visualization? As the first keynote speaker, Hadley Wickham, pointed out most of us has a very different perception on what it actually means.

As the workshop touched upon topics varying from DNA to ecosystems there are also many ways to visualize them. Regardless of the field of study, Hadley Wickham recommended to ‘firstly, think about the data’. The main goal is to decide on a message and a story behind the findings. After answering these fundamental questions one can start looking for the best means to visualize them.

Biological data is complex

Following his recommendation, let’s take a look at data presented during the conference. It was not surprising to learn that biological data is, quite simply, complex – regardless of whether one studies genomes, proteins or tissues. Philippe Collas discussed the complexity of a genome, composed of various elements, that forms different structures.  He made a point by saying that ‘three dimensions (3D) matters’ and an image is just a representation of a real case scenario.

Life happens in 3D so images cause danger of misinterpretation

Almost all the speakers mentioned that life happens in 3D, which causes many struggles in the visualization and interpretation of data. When Lucy Collinson introduced electron microscopy data she emphasized that 2D views (such as images) of 3D scenes (such as proteins) can be misinterpreted.

However, this problem concerns all biological fields. For example, Philippe Collas and Andy Yates discussed the complexity of a genome. Susan Clark presented how the 3D organization of epigenome is disrupted in cancer.

Moreover, Marc Baaden tackled the difficulties of recapitulating dynamics in a static image. In contrast, Loïc Royer showed 4D videos of morphogenesis and challenges with microscopes such as focus or stabilization of images as well as the importance of digital image processing.

Data and visualizations need to be cleaned and structured

In order to form the main message of a discovery, one needs to understand the complexity of data. Many speakers advised to clean and structure data as a first step of analysis. Here, Moritz Stefaner showed the image from Ursus Wehrli ‘The Art of Clean Up’ to represent the art of tidying up.

What’s more, structuring your visualization will help an audience understand the concept better. Hadley Wickham believes that orthogonal components make it easier to compare and remember (in this case using purr library in R).

Data analysis needs to be well documented (preferably in a form of code)

It is obvious that the analysis of biological data is not trivial.  What’s more, one set of data may lead to many different observations. Most of the speakers drew attention to the importance of documenting data and pipelines of analysis. Many advised to use codes. ‘A code is readable, reproducible text’ as Hadley Wickham presented. Most scientists, especially those from RNA and DNA fields such Charlotte Soneson, Irmtraud Meyer and Wolfgang Huber, shared the same opinion.

Data needs story for visualization

Now, when data is cleaned and tackled it is time to decide on the message and a story. Then, one can investigate possible ways of visualizing the findings. How can one find the best way to visualize data? Probably the most common advice was by trial and error, learning what others do, using design concepts, consulting with others. However, if you really have a clear purpose it will be much easier. Moritz Stefaner also believes that scientists have too much trust in the defaults. For example, he showed that rainbow gradient is not necessarily the best one!

Data analysis and visualization need iterations

According to Moritz Stefaner, Loïc Royer and Hadley Wickham, iterations are the key for a good data analysis and visualization. Prototyping and modifying should be a habit of all scientists. Only by iterating can we create something of great value and importance. One needs to ‘create a bunch of bad visualizations that need to be iterated as long as you find the best solution’ Hadley Wickham summarized.

Illustrations and animations capture the complexity of data

As mentioned above, the VIZBI society cares and makes an effort to prepare good visualizations. They believe that visualization is the key to every communication – illustrations and animations make a concept easier to understand. A recipient is able to grasp a research idea much faster. Janet Iwasa also showed that animation enables showing the complexity of biological data as they are in 3D. It can make a hypothesis more accurate and discoveries much clearer. She compared a model figure with a snapshot of her animation to illustrate the difference in perception.  What’s more, to make an animation one needs to fully understand a concept to illustrate it, which makes a finding more precise.

Conclusions

To conclude, although at first sight it seems that all VIZBI session are very diverse, in fact they have a lot in common. All present ways to visualize biological findings based on data. Having said that, the data and visualization techniques are very versatile, but there is a common pipeline. To make data clear to everyone the clue is to find the best way to visualize it by iterating and modifying different solutions. In order to find the best means we need to focus on a main message and story. To create a story we need to fully understand the data by cleaning, structuring and analyzing. Keeping a good documentation in the form of codes, storyboards and notes make findings transparent and reproducible to others. Communication is key in the progress of science, and scientists can improve their visualization methods and skills. VIZBI participants believe that it is worth putting in a lot of effort to make data more understandable and memorable.

Remember to have fun and use your creativity! I definitely had a lot of fun as an event reporter at the 2019 VIZBI workshop, and will incorporate all these lessons in my daily research.

If you have any questions or would like to discuss biological data visualization, please write me a message.

All the images were taken during the conference using private phone. All the images are set to presenter’s names. There are no images of slides that presenters asked not to tweet about.

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Celebrating 15 years of BioMalPar

In honour of World Malaria Day and ahead of the 15th annual EMBL conference on the Biology and Pathology of the Malaria Parasite (BioMalPar), we spoke to the conference organisers Richárd Bártfai, Kirk Deitsch and Lyn-Marie Birkholtz, as well as Andy Waters from the BioMalPar steering committee – which is responsible for selecting the scientific organisers each year – to find out where the field is heading.

Richárd Bártfai, Lyn-Marie Birkholtz, Kirk Deitsch and Andy Waters

 

The BioMalPar conference is celebrating its 15th anniversary this year. How did it all start and how has it developed over the years?

AW: I was part of the organisation of the original meeting in 2004 and have attended every iteration since.  It was originally a dual-purpose meeting designed to bring together the participants in the EC funded Network of Excellence of the same name, “BioMalPar”, the students in the associated PhD school that it funded, and to serve as an international meeting on malaria.

LB: I started attending BioMalPar in 2006 and was inspired by the format of the conference, allowing such great interaction and exposure to young scientists. It always allows the most cutting edge (mostly unpublished) research to be presented, and the addition of workshops to the conference programme allows for additional opportunities for learning, and these workshops are new and trending every year.

2018 BioMalPar conference at the EMBL Advanced Training Centre

What inspired you to organise this conference?

LB: This meeting to me is THE malaria conference that I annually attend. As a researcher from a malaria endemic country, I was inspired to organise the conference to strengthen exposure of the great research performed in such countries at the conference, and provide context for the research findings to show how the excellent research presented have direct impact to people’s lives living with malaria.

RB: This meeting is a prime example of a community effort. Hence organising it is an honour and a great way to serve our community. I very much enjoyed the collegial and welcoming atmosphere created by former organisers and I hope that we will manage to recreate some of it this year as well.

KD: In recent years, the conference has become more widely attended by non-European scientists and is now an event attended by investigators from throughout the world. When I was invited to participate in the organisation of this year’s meeting, I considered it an exceptional opportunity to interact with international colleagues and build stronger ties for exchanging ideas and potential collaborations.

The format of the conference is a bit distinct from that of other meetings in that the majority of talks are reserved for selected short talks. What is the benefit for the programme to have mostly selected talks?

KD: Reserving the majority of each session for short talks ensures that the latest, unpublished data will be presented at the meeting. Highlighting young investigators presenting new data for the first time also lends an air of excitement to the sessions that adds to the overall “buzz” of the conference.

LB: This is in my opinion one of the main strengths of the conference. The audience will have the ability to hear new data ‘straight from the horses mouth’ as the short talks are mostly presented by early career scientists and mostly covers unpublished work.

AW: The emphasis is on packing in as much new science by the early career researchers as possible.  This format makes it possible and allows one to work to themes in terms of the meeting organisation

RB: We will have excellent keynote lectures this year to set the stage and provide broad overviews on specific subjects. Yet, selected talks offer opportunity to young research fellows to share their exciting, unpublished findings.

The poster sessions allow researchers to present their findings

The short talk selection for this year’s edition has now been finalised. Could you share what the focus and highlights of the conference will be?

RB: The content of the short talks is traditionally kept secret till the start of the meeting and I do not want to break this tradition ;-). But we as organisers had a hard time to make a selection out of the numerous excellent abstracts submitted, so I am certain that the scientific standard of the meeting will be very high.

LB: As organisers, we were very happy to have a large basis of excellent abstracts to select from, which will make the final choices exciting to come and listen to!

In your opinion, what challenges is malaria research facing and how close are we to an effective malaria vaccine?

KD: Everyone in the field is thrilled that a malaria vaccine is now being deployed for the first time. However, we also recognise that this vaccine has significant shortcomings in terms of its efficacy and longevity of protection. Research into the nature of the immune response of people infected by malaria parasites, as well as identifying new drugs and drug targets and methods of vector control will all contribute to our ability to control the disease.

LB: With the trial roll out of the RTS,S malaria vaccine in Malawi, we are indeed closer to evaluating the large scale effect of this intervention. However, malaria is a very complicated disease and we should continue with our multifaceted integrative control strategies, which will possibly be the only way we can really have an impact towards elimination. Our research challenges remain to inform policy makers as to the importance of continued funding of the work and for the research community to continue translating these to tangible outcomes, as we have done successfully for the past decade.

RB: Despite substantial progress in the last decades elimination of malaria is still out of our reach. Integration of insight gained in various fields will be essential for generating breakthroughs in drug/vaccine development and vector control alike. The BioMalPar meeting certainly provides an excellent platform for the exchange of innovative ideas and hence will help to bring the well-desired goal of malaria elimination closer to reality.

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Easter with Buddy

We decided that in 2019 – for no other purpose than to make Buddy feel included at Easter time – we would create a Buddy pancake for Shrove Tuesday, aka “Pancake Day”.

Having enlisted the help of some very competent pancake makers (aged 3 and 6), we got to work creating our masterpiece.

After studying the subject in great details (i.e. we looked at some photos of Buddy on Instagram), we mixed the batter that would shape Buddy. After making the first few pancakes, we started sculpting. Although we may not have made the shape to perfection, the two pancake makers were more than satisfied!

Decorating Buddy got a bit messy, but we made it in the end. Some ricotta cheese served as “glue” for our green spinach, yellow mango and purple Serrano ham.

And here you have it – our very own Buddy Pancake! Not only does he look like our favourite little yeast cell, but he was also surprisingly delicious! Well, for the grownups at least – the pancake makers drew the line at the thought of eating spinach!

Buddy the pancake vs. Buddy the doll – can you even tell the difference?!

The Recipe:
We took the basic pancake recipe from here:

https://www.bbc.com/food/recipes/basicpancakeswithsuga_66226

Apparently we are big pancake fans, as we multiplied this recipe by three and it was just right for a family of four!

Unfortunately he didn’t last long!
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One language to unite them all

Copyright: EMBL Photolab

And so it became that the whole earth was of many languages, with no common speech. As people moved to Germany, they found a hill in Heidelberg and settled there.

They used steel and glass instead of stone, and cement for mortar to build their settlement. Then they said, “Come, let us build ourselves a campus, with a tower of DNA that reaches to the heavens, so that we may make a name for ourselves; otherwise we will be scattered over the face of the whole earth.”

Then the Director General came down to see the campus and the tower the people were building. The Director General said, “If as one people speaking different languages they have begun to do this, then nothing they plan to do will be impossible for them. Come, let us go down and give them one language so they will understand each other even better.”

So the Director General gathered them there from over all the earth, and gave them the language of science and they finished building the campus and the tower. It is now called the Tower of ATC – because there people from the whole world gather to speak the universal language of science and do great things.*

We speak over 40 different languages at EMBL but we all speak the language of science. Happy International Mother Language Day (21 February)!

*The text was adapted from Genesis 11:1-8, New International Version.

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Organoids: Modelling Organ Development and Disease in 3D Culture

EMBO | EMBL Symposium – Heidelberg, 10-13 September 2018
Meeting report by Veronica Foletto

Following the huge success of the 2016 symposium ‘Organoids: Modelling Organ Development and Disease in 3D Culture’, Hans Clevers, Jürgen Knoblich, Melissa Little, and Esther Schnapp joined forces to organise a second such symposium this year. On the afternoon of 10 September, 460 scientists from all over the world gathered in the auditorium of the EMBL Advanced Training Centre (ATC) in Heidelberg.

Hans Clevers, a leading expert on organoids, welcomed everyone and led the opening session. The first keynote lecture was given by Jürgen Knoblich, who reported on progress in his lab using cerebral organoids to model the complexity of the human brain and, in particular, to study microcephaly. The subsequent talks showed how organoids derived from different tissues provide useful models for the recapitulation of certain diseases such as Helicobacter pylori infection and secretion of the VacA toxin in the stomach, as discussed by Xuebiao Yao or models of early development, with Nicolas Rivron introducing the blastoid: a type of organoid similar to an early embryo, which can be used to study developmental processes in 3D.

The second day began early with an interesting ‘Meet the Editors’ session, in which scientists had the chance to talk directly to editors working for many scientific publishers (Springer, Nature, The Company of Biologists, Wiley, Cell Press and EMBO press) and to understand their vision.

Afterwards, Meritxell Huch chaired the session ‘Stem Cells and Development’, in which scientists presented advancements in the use of cerebral (Wieland Huttner) and pancreatic (Anne Grapin-Botton) organoids for deciphering cellular mechanisms during human development, and of gastruloids for studying the patterning of the antero-posterior axis (Denis Duboule). Near the end of the session, Bon-Kyoung Koo described how to efficiently use CRISPR technology to perform genetic studies in intestinal organoids. The session ended with a series of 2-minute flash talks, after which networking and interactions were encouraged during lunch, where there was an opportunity to meet the day’s speakers.

The beautiful helices of the ATC then provided the venue for the first poster session, where around 90 presenters had the chance to discuss their research with fellow scientists, editors, and a scientific evaluating committee. It was absolutely inspiring to see how many people work on organoid research!

The afternoon session, ‘Organoids from tissue stem cells’, included talks on organoids derived from taste stem cells (Peihua Jiang), cochlear cells (Albert Edge), and intestinal cells (Hans Clevers). Madeline Lancaster explored the possibility of studying differentiated human cerebral organoids which self-assemble in the stereotypic organisation of the early human embryonic brain and have functional motor-neuronal circuits.

Among this ‘zoo of organoids’ as humorously defined by Jürgen Knoblich there was room for organoids derived from snake venom glands (Yorick Post): the organoid toolbox seems to be extendable to non-mammalian cultures as well!

On Wednesday morning, James Wells introduced the session ‘Recreating organs from pluripotent stem cells’. This addressed cell fate decisions in the developing mouse thyroid gland or lung (Sabine Costagliola), the human lung (Jason Spence and Hans-Willem Snoeck), the human salivary gland (Cecilia Rocchi), and the human forebrain (Flora Vaccarino), studied primarily through single-cell transcriptome and enhancer analyses. Finally, it was the turn of Mathew Garnett, who started by showing that the worldwide number of new cases of cancer each year is around twice the population of Switzerland.

Interested in using precision organoid models to study cancer and patients’ responses to treatment, Garnett is now contributing to the development of the Human Cancer Models Initiative. Its goal is to create a new generation of molecularly annotated cancer models, which will be widely beneficial to the scientific community.

After the second poster session, there were talks on ‘Organoids and disease modelling’, introduced by Anne Grapin-Botton. Among the topics covered were the use of 3D organoids to model liver regeneration and disease (Meritxell Huch), and to study cancers of the bladder (Michael Shen), pancreas (David Tuveson), breast (Martin Jechlinger), and colon (Henner Farin).

The day ended beautifully with the conference dinner in the EMBL canteen and the delightful live music that brought together the diverse group of researchers once again.

The final day of the conference was dedicated to ‘Cells and materials in regenerative medicine’. Matthias Lutolf discussed some of the ongoing efforts in his research group to develop next-generation organoids through tissue engineering. Meritxell Cutrona reported advances in nanoparticle tracking in 3D structures, which is particularly useful for drug delivery. Lakmali Atapattu described 3D bioprinting of tumoroids. Henrik Renner presented a high throughput-compatible workflow for the generation, culture, and optical analysis of neural human organoids. Rob Coppes and Melissa Little reported on promising progress in improving cancer treatment, using glandular and kidney organoids, respectively. James Wells gave a talk on the applications of gastrointestinal organoids, concluding with some food for thought for the audience: “It is better to collaborate, than to compete.”

The Symposium ended with the poster prizes, sponsored by EMBO Reports, EMBO Molecular Medicine, and Sartorius. Personally, I found these four days extremely stimulating, full of opportunities for interaction and discussion. I believe most of my fellow researchers got the same feeling: 3D organoid systems are revolutionising molecular biology and driving the development of better clinical therapies, and we are all contributing to this revolution.

What will we be able to achieve with organoids in two years’ time?

Stay tuned, the meeting will be back in 2020!

@LunardiLabCIBIO

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