3rd BiVi Annual Meeting Programme

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Thursday 20th April

09:30-10:00    Registration

Presented by Jean-luc Doumont, Principae, Belgium
Chaired by Jessie Kennedy

Useful as each of them can be, a large body of tips and tricks is impossible to remember, at least in a practical, usable way, unless it is structured into a balanced, meaningful hierarchy. This talk proposes and illustrates three simple yet solid ideas that lead to more effective communication and that underpin every other guideline: easy to remember, readily applicable, and always relevant—in short, valuable for the rest of your life.

This keynote will be open to the public

An engineer (Louvain) and PhD in applied physics (Stanford), Jean-luc Doumont is acclaimed worldwide for his no-nonsense approach, his highly applicable, often life-changing recommendations on a wide range of topics, and Trees, maps, and theorems, his book about "effective communication for rational minds". For additional information, visit www.principiae.be.

11:00-11:30    Coffee and Late Registration

11:30-12:30    UK Bio-visualisation Part 1 - chaired by Richard Baldock

Zegami has the potential to do for images what the spreadsheet did for number calculations. It provides a way of manipulating images and derived values (from the images themselves or annotated metadata) on a massive scale allowing querying and organisation of large image based collections. The talk will show various examples of its usage in biology and beyond, and will look at new features such as annotation to build training sets for machine learning.

Presented by Stephen Taylor, Weatherall Institute of Molecular Medicine, University of Oxford

Read more about Zegami
This talk will report how our research on protein modelling has led to the development of computer games with a role in scientific education.

At Imperial, Chris Reynolds has developed a web-based molecular graphics resource EzMol which is a simple-to-use display of protein structures. In collaboration with Frederic Fol Leymarie, William Latham and their team at Goldsmiths, we have developed the BioBlox suite of scientific-based computer games based around protein docking. BioBox3D is a serious crowd-sourced game for predicting protein/protein docking. BioBlox2D is a fun-to-play game with scientific content for phone/tablet inspired by the recognition between proteins and small molecules. Finally, BioBloxVR is a virtual reality environment for protein docking inspired by BioBlox3D. We are exploring the opportunities for EzMol and BioBlox as educational resources. The projects were supported by the BBSRC.

Presented by Mike Sternberg, Department of Life Science, Imperial College London

12:30-13:30    Lunch at The Chapel, Craiglockhart

Presented by Marc Streit, Institute of Computer Graphics, Johannes Kepler University Linz
Chaired by Tom Freeman

The primary goal of visual data exploration tools is to enable the discovery of new insights. To justify and reproduce insights, the discovery process needs to be documented and communicated. A common approach to documenting and presenting findings is to capture visualizations as images or videos. Images, however, are insufficient for telling the story of a visual discovery, as they lack full provenance information and context. Videos are difficult to produce and edit, particularly due to the nonlinear nature of the exploration process. Most importantly, however, neither approach provides the opportunity to return to any point in the exploration in order to review the state of the visualization in detail or to conduct additional analyses.

In this talk, I will introduce our efforts to more tightly integrate biomedical data exploration with the presentation of discoveries. Based on provenance data captured during the exploration process, users can extract key steps, add annotations, and author 'Vistories', visual stories based on the history of the exploration. These Vistories can be shared for others to view, but also to retrace and extend the original analysis. I will demonstrate how such methods can increase the reproducibility of cancer research and drug discovery.

The presented work is part of the Caleydo project, which is a long-running collaboration between JKU Linz, Harvard University and the University of Utah.

Marc Streit is a tenured Associate Professor at the Institute of Computer Graphics at Johannes Kepler University Linz where he leads the Visual Data Science group. He finished his PhD at the Institute for Computer Graphics and Vision at Graz University of Technology in early 2011 and moved to Linz later that year. In 2012 he was a visiting researcher at the Center for Biomedical Informatics (CBMI) at Harvard Medical School. As part of a Fulbright scholarship for research and lecturing he was a visiting professor at the Visual Computing Group at Harvard Paulson School in 2014. Marc also teaches courses at the Imperial College Business School and Salzburg University of Applied Sciences.

His scientific areas of interest include visualization, visual analytics, and biological data visualization, where he is particularly interested in the integrated analysis of large heterogeneous data. Together with his team he develops novel visual analysis tools for cancer research, drug discovery, and other biomedical applications. Most of his research is embedded in the open-source project Caleydo, where he is one of the project leaders and founding-members. Since 2016 he is a CEO of the JKU spin-off company datavisyn.

Marc won Best Paper Awards at InfoVis'13, BioVis’12, InfoVis’11, GI’10 and Honorable Mention Awards at EuroVis'16, CHI'14, InfoVis'14 and EuroVis’12. He is a co-author of the Nature Methods Points of View column. In 2013 he co-edited the Special Issue on Visual Analytics in the IEEE Computer journal. Additionally, he actively contributes to the scientific community by serving on the organizing and program committee of several scientific events as well as by acting as a reviewer for high-quality journals and conferences. He was program chair of the IEEE Visualization in Data Science Symposium and papers and now general chair of BioVis, the Symposium on Biological Data Visualization.

14:30-14:50    Coffee

14:50-16:10    UK Bio-visualisation Part 2 - chaired by Mike Sternberg

The increasing scale and complexity of genome scale studies has led to more widespread use of unsupervised analysis pipelines and reduced inspection and sanity checking of the underlying data. Here we will illustrate how the use of interactive visualisation tools along with an explorative approach to analysis can identify problems which would otherwise go undetected by standard pipelines.

Presented by Simon Andrews, Babraham Institute
Reactome provides curated human biological pathways representing the consensus view of the molecular events involved. Pathway Diagrams show mechanistic details, using a style based on SBGN. A unique Overview represents all pathways in a single view. Analysis results and expression data are represented in both Pathway Diagrams and Overview as coloured overlays.

Presented by Steve Jupe, EMBL-EBI

Read more about Reactome
Genetic and environmental variation affect all complex human traits and disorders. Recent large-scale genome-wide association studies have identified some of the specific genetic variants, and we often assume these associations will hold true irrespective of context. However, our research shows that the relationship between genotype and phenotype can change across a lifetime or in different environments. For example, some genetic variants may have larger effects in adulthood or in the centre of cities. Data visualisation plays a vital role in bringing researchers together across disciplines to understand these dynamic patterns of gene-environment interaction.

Presented by Oliver Davis, University of Bristol
Unfortunately this talk has been cancelled.

Presented by David Aanensen, Wellcome Trust Sanger Institute & Imperial College London

16:10-16:40    Lightning Talks - chaired by Jim Procter

16:40-17:00    Coffee

Presented by Bang Wong, Broad Institute of MIT & Harvard and Department of Art as Applied to Medicine, Johns Hopkins University School of Medicine
Chaired by: Geoff Barton

The data generated by the biomedical research community hold tremendous potential to inform our understanding and treatment of disease. The challenge is to ensure that technical and non-technical researchers can access, use and learn from this wealth of data and analytical resources. I will present examples of solutions developed at the Broad Institute that draw on art and design to enable scientific discovery.

This keynote will be open to the public

Bang Wong is the creative director of the Broad Institute of MIT & Harvard and an adjunct assistant professor in the Department of Art as Applied to Medicine at the Johns Hopkins University School of Medicine. His work focuses on the design and development of computation-visualization tools to meet the analytical challenges of research data. He leads the data visualization initiative at the Broad and is the founding author of Points of View published by Nature Methods, a series of articles that focus on the fundamental aspects of data presentation in science.

18:00-19:30    Reception and Poster Session, The Chapel, Craiglockhart

19:30     BiVi Dinner at the Rivers Suite, Craiglockhart

All presentations will take place in the Lindsay Stewart Lecture Theatre, Craiglockhart.


Friday 21st April

09:30-10:45    Training / Workshops

10:45-11:15    Coffee

11:15-12:30    Training / Workshops

12:30-13:30    Lunch at The Chapel, Craiglockhart

13:30-14:45    Training / Workshops

14:45-15:15    Coffee

15:15-16:30    Training / Workshops

16:30              Meeting Close

Workshop Options:

09:30-10:45 11:15-12:30 12:30-13:30 13:30-14:45 15:15-16:30
MARender - Richard Baldock Gene Expression Commons - Jun Seita   Reactome - Steve Jupe
Aequetas with Galaxy - Anil Thanki   SeqMonk - Simon Andrews
Visualisation with Python - Martin Jones   Miru - Tom Freeman
    Jalview - Jim Procter
Creating data visualisations - Jan Aerts & Marc Streit

Workshop locations will take place in individual rooms at Craiglockhart. Room details will be available at the meeting.