Meet the Trainer – Andrew Filby

Meet Dr. Andrew Filby, Director of the Flow Cytometry Core Facility at Newcastle University, which supports cutting-edge research through the provision of a comprehensive cytomics resource to both internal and external research groups, operating at the forefront of cytometric applications and method-focused research. Andrew Filby is one of the organisers of the EMBO Practical Course: The Fundamentals of High-End Cell Sorting (11 – 15 November 2019).

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

The ability to physically separate (sort) cells of a particular type or subtype is fundamental in so many biological questions. Teaching and empowering researchers how to do this well is very important.

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

Cell sorting can be used for so many different reasons, ranging from basic discovery research right through to clinical trials and cell therapies.

Are the methods used in this course unusual or new?

Cell sorting has been around since the 1960s and the principles remain quite stable. However, in this course we teach students the practical as well as the theoretical aspects. The course is run by experts in the field and in a “real world” environment where attendees will be trained in two functioning flow cytometry/cell sorting core facilities.

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

Everything about EMBL is set up for delivering excellent training in biological sciences and in particular the practical, hands-on elements. The training labs are amazing spaces and looked after very well. The canteen is also a highlight!

What is your number one tip related to the course?

Roll your sleeves up and get involved. Ask questions and interact with your trainers as much as possible.

What is your research focus, in 15 words or less?

I want to measure everything about every cell in the body!

What challenges is your research field facing?

The data we generate now is very complex. We have thousands of measurements on millions of cells, sometimes with image and spatial information too. The informatics skills and solutions needed can be immense.

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

The invention of the cell sorter!

If you were a superhero what power would you have?

I would like to shrink myself so that I could travel around the human body and see the cells and processes for myself.

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

 

 

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.

6 ways to enhance your scientific career with networking and informational interviews

Do you want to know how networking and informational interviews can enhance your scientific career? Are you unsure of whether to stay in academia or not? Find out how to use your contacts and professional networking sites to find and obtain the right job for you.

  1. Use your personal contacts

Use existing contacts to get first hand, tailored information from people who’ve made the transition into different types of careers. You might also be a member of different networks such as an alumni association or a scientific society where you can find people to talk to about their careers, or perhaps you are attending a conference where you can speak to people directly about their experiences.

  1. Don’t be afraid of professional networking sites

Make the most of what’s on offer, be it LinkedIn, ResearchGate, Xing or other local sites. Search for people who have similar skills or backgrounds as you, contact them and ask if they’d be willing to talk to you about their career. Join groups on these sites to talk to people in similar fields as you are in or want to get into.

  1. Set up some “informational interviews”

An informational interview is an informal discussion about careers where you can get advice and information – it is not something that will lead to a job but should rather be a source of inspiration and advice. Get in touch with the people who might be able to offer you some sound advice, and ask if they can spare 20 minutes for you to pick their brains.

  1. Prepare for your informal interview

One way to structure these informational interviews is to use REVEAL*:

  • Recap – Who are you and why would you like to talk to this person
  • Explore – Prepare questions to help you explore the career area, role and sector
  • Vision – Follow up with more detailed questions about the trends for the field, and where your career could head in the longer term
  • Entry Routes – How did the person you’re talking to get into the role? Are there different routes to getting in?
  • Action Points – What do you need to do to get these kinds of roles? Can also ask for feedback on your CV
  • Links – Can the person recommend any other resources to you?
  1. Realistically assess your skills, values and interests

Scientists often struggle with working out what kinds of jobs they are best suited to. Look in depth at your skills, values and interests. Use this information to filter your career research. You can, for example, look for people with a similar skill set on LinkedIn and see what kinds of roles they have and gain some inspiration for what you might be interested in.

  1. Research the available career possibilities

There are a large variety of options out there for scientists who don’t want to stay on the academic career path. In addition to research in pharma, biotechs and startups there are also a variety of roles where you can use your scientific knowledge, understanding of the research process or data analysis skills. These roles often support scientific research, communicate research findings more broadly, or help translate research into real life applications.

Resources

Original video with Rachel Graf, EIPOD Career Advisor, EMBL Heidelberg

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.