PeerJ Award Winners at VIZBI 2021

Continuing our collaboration with the VIZBI conference series, PeerJ recently sponsored two awards to highlight the best posters that were presented as part of VIZBI2021 – the 11th international meeting on Visualizing Biological Data. We talked to the researchers behind these posters to find out more about their work and how they become involved in the science of visualizing data.

Martina Maritan Postdoc at Scripps Research, San Diego, USA.

Full Poster: https://vizbi.org/Posters/2021/vB26

Lightning Talk: https://vizbi.org/Lightning/2021/vB26

Can you tell us a bit about yourself and your research interests?

I am a computational structural biologist with a passion for science illustration. I started my academic career with a Ph.D. in X-ray crystallography, which gave me the chance to appreciate the beauty of the molecular world. As a crystallographer, I would stare at protein structures for hours and spend a lot of time creating eye-catching visuals to communicate my findings. I realized that art and science go hand-in-hand and fell in love with the process of creating informative illustrations that highlight the beauty of science. Visualization was essential to achieve these goals. This experience sparked my interest in molecular graphics and I found my current lab at Scripps Research to be the perfect fit for me. Here my research focuses on ways to build and navigate cellular scenes in 3D. I also collaborate with the scientific illustration studio 3D Protein Imaging to fuel my more artistic and creative side.

Can you briefly explain the research you presented at VIZBI 2021?

The poster I presented at VIZBI is about spatial mesoscale modeling and how we build the 3D model of a whole cell. We chose a bacterial cell to test and refine our methods (CellPACK, Mesoscope, LattinceNucleoid). From the experimental standpoint, there is not a single technique able to capture the range of scales called the mesoscale, which makes it a perfect domain for integrative structural modeling. We generated a collection of structural models for all the protein components of the bacterial cell of interest and a 3D model of its genome, we put all those elements together in the first atomistic representation of an entire bacterial cell. I had a fun time during the presentation doing some live demonstration of how interactively navigate our model with CellPACK, there is a sneak-peak in my lightning talk. Mesoscale models can have the potential to be interrogated over specific biological questions and to be used as tools for hypothesis generation.

What first interested you in this field of research?

During my Ph.D., I was using molecular graphics to discover the secrets of my proteins and I found it to be such a powerful way to study science and boost my level of understanding. I was fascinated by how heavily visuals impacted my comprehension and I wanted to know more about this field of research and, most of all, be a part of it. Like many others, I was amazed by the molecular paintings of David Goodsell. The first time I saw one of those art pieces I thought ‘so there are people that do this as part of their research? Why am I still here crystallizing proteins? I want to do that!’.

What do you like about this field of research?

What we do is reconstruct the complexity of a living cell visually in a computer, so the answer to this question is: do you know anything cooler than that? I don’t! Being able to build a model that depicts an entire cell is extremely exciting because it opens so many new questions on cell functioning and shows how all cellular systems are interconnected. I think what makes me enthusiastic is that we are trying to integrate information coming from many different disciplines and tackling challenge after challenge in the field of mesoscale research. My dream is that one day we will have a realistic representation of all cells and we will be able to take tours inside of them, maybe in VR!

How did you find the virtual conference experience?

First of all, I think VIZBI is such an exciting and inspiring conference that no matter the format, it is always amazing! There were a surprising amount of moments for networking and spontaneous discussion, such as the breakout sessions to the art&biology event. I was very impressed with the VIZBI organization. It has been the best virtual event I have attended so far! I think online conferences have been a great alternative during the pandemic, allowing participation from all over the world. However, personally, I prefer to meet and talk to people in person. I do appreciate the accessibility of online events, but I look forward to going back to old-school conferences.

What are your next steps? How will you continue to build on this research?

The next steps will be using CellPACK to create new mesoscale models of different organisms, with the aim of being able to simulate them and use them as tools in biomedical research. I am now wrapping up this part of the project in a publication. Being awarded for the Best Scientific Poster allowed my work to be seen by many scientists and I hope it will attract new collaborations and ideas for mesoscale modeling applications. I also plan to keep working with 3D Protein Imaging and to take on more scientific illustration projects to express my creativity and passion for communicating the beauty of science!

How can we keep up with your work?

You can follow my personal social media channels:

Twitter: https://twitter.com/MartinaMaritan

LinkedIn: https://www.linkedin.com/in/martina-maritan/

Or 3D Protein Imaging social media:

Instagram: https://www.instagram.com/proteinimaging/

Twitter: https://twitter.com/proteinimaging

Website: https://3dproteinimaging.com/

Christian Stolte Lead Visualization Engineer at Cellarity, Cambridge, USA.

Poster: https://vizbi.org/Posters/2021/vA21

Lightning Talk: https://vizbi.org/Lightning/2021/vA21

Can you tell us a bit about yourself and your research interests?

I began my career as an artist and designer, and got started in science through designing websites and tools for genomic data, initially at the Broad Institute. Then I worked at CSIRO in Sydney, Australia, and the New York Genome Center, and became involved in the biological data visualization community through the VIZBI conference series. I am interested in how design can improve tools for life science research and enable new insights through bespoke visualizations. I strive to represent data in ways that are clear and intuitive while embracing complexity.

Can you briefly explain the research you presented at VIZBI 2021?

Cellarity is pioneering a new approach to drug discovery, treating disease at the level of the cell as opposed to a single molecular target. Combining unique expertise in network biology, high-resolution single-cell sequencing data, and machine learning, the result is a new understanding of the cell’s trajectory from health to disease. The cell and its network of transcripts and proteins offer a more complete view of the complexity of human biology than any individual molecular target. To help communicate this, we use visualizations resembling a cityscape called “Cellarity maps”.

Tell us more about Cellarity Maps

The process begins with a UMAP plot (“Uniform Manifold Approximation and Projection”), which is a technique for representing high-dimensional data, such as single-cell gene expression measurements for thousands of genes per cell, in a two-dimensional scatterplot that encodes cell behavior. Cells with similar attributes come to lie next to each other; those with large differences are rendered far apart. The density of points in the plot is difficult to see in 2D, but when translated into 3D —the height of those towers— it becomes obvious. This creates landscapes that can now be painted with color to infuse meaning, and make it easier to see different ‘cell behaviors’. The idea to represent cell populations as 3D density plots that look like modern cityscapes was developed by Milind Kamkolkar and Nick Plugis at Cellarity, together with Dani Bergey from Cognition Studios in Seattle. They used them primarily for communicating Cellarity’s science to the public on the website. When I joined Cellarity in January 2021, I thought those plots could be useful for research, too: if we made an interactive tool where people can inspect the maps from all angles, load different datasets and compare them, we can use color as a channel to show additional dimensions, such as cell states or gene expression values.

What first interested you in this field of research?

I was always interested in science, but when I discovered that data visualization and visual analytics were a real ‘thing’, I was hooked. For me it’s the perfect combination of art, design, and science.

How did you find the virtual conference experience?

I loved the way the organizers combined Zoom with breakout rooms, Slack, and Gather to create a social atmosphere. The applause at the end of each talk was a nice touch. But especially having Gather, as a space where you could hang out and run into people, almost made me feel like I was at a physical meeting. I actually met people and made some new friends — it was great!

What are your next steps? How will you continue to build on this research?

I am working on a suite of data exploration and analysis tools for Cellarity that integrate into a larger context and help people from different disciplines collaborate. Combining machine learning with visual analytics holds so much promise for tackling the immense complexity of biology, and I’m excited to be part of a team that explores that territory.

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For more VIZBI award winners head to https://peerj.com/blog/post/115284883237/peerj-award-winner-beata-mierzwa-best-scientific-poster-award-at-vizbi-2019/

If you are organizing a conference or workshop and would like to offer a PeerJ Award at your event, please let us know – communities@peerj.com