Program BioVis@ISMB

BioVis@ISMB 2021 Program

July 26-27, 2021

Invited Speakers

Theories of inference for visualization interactions
Jessica Hullman, Northwestern University
Jessica Hullman
Abstract: Research and development in computer science and statistics have produced increasingly sophisticated software interfaces for interactive and exploratory analysis, optimized for easy pattern finding and data exposure. But design philosophies that emphasize exploration over other phases of analysis risk confusing a need for flexibility with a conclusion that exploratory visual analysis is inherently “model free” and cannot be formalized. We describe how without a grounding in theories of human statistical inference, research in exploratory visual analysis can lead to contradictory interface objectives and representations of uncertainty that can discourage users from drawing valid inferences. We discuss how the concept of a model check in a Bayesian statistical framework unites exploratory and confirmatory analysis, and how this understanding relates to other proposed theories of graphical inference. Viewing interactive analysis as driven by model checks suggests new directions for software and empirical research around exploratory and visual analysis.
Bio: Jessica Hullman is an Associate Professor of Computer Science and Journalism at Northwestern University. Her research develops new representations, interactions, and evaluation methods for aiding people in analyzing and visualizing data to amplify cognition and decision making. Her recent research also addresses theories of data analysis and science reform. She founded and co-directs the Midwest Uncertainty Collective, a lab devoted to better visualization techniques, tools, evaluations, and theory around how to communicate uncertainty in data. Jessica is the recipient of a Microsoft Faculty Fellowship, NSF CAREER Award, and multiple best papers at top visualization and human-computer interaction conferences, among other awards.

Inter-disciplinary practices in BioVis
Seán O’Donoghue, Garvan Institute of Medical Research
Seán O’Donoghue
Abstract: BioVis involves a diverse community; while many of us are computer scientists, bioinformaticians, or bench biologists, our field also engages designers and illustrators, and our outcomes are used by students, educators, and science communicators. In this talk, I will highlight work practices used in inter-disciplinary collaborations to address key BioVis challenges. In addition to drawing on historical exemplars, I will showcase how I have used these practices in recent collaborative work on (a) human genetic variations, (b) multi-omics time-series studies, (c) the SARS-CoV-2 proteome, and (d) exploring protein structures with extended reality. I will also discuss how these practises influence the emergence of BioVis as a recognized discipline.
Bio: Seán O’Donoghue leads the BioVis Centre (http://odonoghuelab.org/) based at the Garvan Institute of Medical Research in Sydney, Australia. He is also chief editor of the Data Visualization section of the Frontiers in Bioinformatics journal. Formerly, he was also an OCE Science Leader and a Chief Research Scientist in Australia's CSIRO. Much of his career was spent at the EMBL in Heidelberg, Germany, and also at EMBL’s first spin-off company, Lion Bioscience AG, where he was Director of Scientific Visualisation. Seán's career has focused on using computational methods to advance the life sciences. His early work was on improving how bimolecular structures are calculated from NMR data; however since 2000 he has focused on data visualization methods. He is co-founder and chair of the 'VIZBI' initiative, aimed at raising the global standard of data visualisation in computational biology. His team have created bioinformatics resources used by tens of thousands of life scientists worldwide, as well as informative and inspirational biomedical animations seen by over half a million people. His current research interests centre on using bioinformatics and data visualisation to better understand the spatial organisation of the genome (e.g., http://rondo.ws/), dynamic changes in the epiproteome (e.g., https://minardo.org/), and the structural biology of the proteome (e.g., https://aquaria.app/) - including the unknown or 'dark' proteome.

Program

Please note that all the times listed here are in Coordinated Universal Time (UTC).


11:00 - 12:20
July 26: BioVis Opening and Keynote
Chair: Michael Krone & Cagatay Turkay
11:00 - 11:10
BioVis Opening
Speaker: Michael Krone & Cagatay Turkay
11:10 - 12:00
[keynote] BioVis Keynote: Inter-disciplinary practices in BioVis
Authors: Seán O’Donoghue
12:00 - 12:20
[invited talk] BioVis 10th Anniversary - Test of Time Award Talk
Authors: G. Elisabeta (Liz) Marai

12:40 - 14:00
July 26: Talk Session-1 (Genomics)
Chair: James Procter
12:40 - 13:00
[proceedings talk] OncoThreads: Visualization of Large Scale Longitudinal Cancer Molecular Data
Authors: Theresa Anisja Harbig, Sabrina Nusrat, Tali Mazor, Qianwen Wang, Alexander Thomson, Hans Bitter, Ethan Cerami and Nils Gehlenborg
13:00 - 13:10
[talk] Visualisation of Identical-By-State regions across multiple assembled genomes
Authors: Ricardo Humberto Ramirez Gonzalez, Jemima Brinton and Cristobal Uauy
13:10 - 13:20
[talk] Visualization of SARS-CoV-2 Genome Atlas
Authors: Kavya Vaddadi, Naina Tiwari, Aditya Rao, Vangala Govindakrishnan Saipradeep, Thomas Joseph, Rajgopal Srinivasan and Naveen Sivadasan
13:20 - 13:30
[talk] A look at trails through the pangenome visualization jungle
Authors: Éloi Durant, Francois Sabot, Matthieu Conte and Mathieu Rouard
13:30 - 13:50
[talk] Grammar-Based Interactive Visualization of Genomics Data
Authors: Sehi L'Yi, Qianwen Wang, Fritz Lekschas and Nils Gehlenborg
13:50 - 14:00
[talk] OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data
Authors: Theresa Anisja Harbig, Julian Fratte, Michael Krone and Kay Nieselt

14:20 - 15:20
July 26: Talk Session-2 (Cells & Omics)
Chair: Liz Marai
14:20 - 14:40
[talk] State-based Visual Analysis of Disease Progression with ThreadStates
Authors: Qianwen Wang, Tali Mazor, Theresa Anisja Harbig, Ethan Cerami and Nils Gehlenborg
14:40 - 15:00
[talk] Vesalius: Image-free extraction and analysis of tissue anatomy by using image processing applied to sequencing base Spatial Transcriptomics
Authors: Patrick Martin
15:00 - 15:20
[highlight talk] BioVis Highlights Talk: Insights From Experiments With Rigor in an EvoBio Design Study
Authors: Jen Rogers

15:20 - 16:20
Poster Hall / Scientific Research Exchange / BoFs

18:00 - 20:00
July 26: BioVis Social Event & Michel Westenberg Memorial
18:00 - 20:00
BioVis Social Event & Michel Westenberg Memorial (will take place in a separate Zoom room announced on the day)

11:00 - 12:20
July 27: Talk Session-3 (Machine Learning)
Chair: Kay Nieselt
11:00 - 11:10
[talk] Benchmarking framework for optimal visualization and interpretability of high-dimensional separable data
Authors: Komlan Atitey and Benedict Anchang
11:10 - 11:30
[talk] Explaining Deep Learning Approaches in Drug Repurposing through Interactive Data Visualization
Authors: Qianwen Wang, Kexin Huang, Payal Chandak, Marinka Zitnik and Nils Gehlenborg
11:30 - 11:40
[talk] Association Plots reveal cluster-specific genes from high-dimensional transcriptome data
Authors: Elzbieta Gralinska and Martin Vingron
11:40 - 11:50
[talk] Color encoding of high-dimensional data using the CIELAB color space and state-of-the-art dimensionality reduction techniques
Authors: Mikaela Koutrouli, John H. Morris and Lars J. Jensen
11:50 - 12:00
[talk] Hierarchical interactive exploration and analysis of single cell RNA-seq datasets
Authors: Jayaram Kancherla, Kazi Tasnim Zinat, Stephanie Hicks and Hector Corrada Bravo
12:00 - 12:20
[highlight talk] BioVis Highlights Talk: Image visualisation in publications - current status and workflows for improvements
Authors: Helena Jambor

12:40 - 14:00
July 27: Talk Session-4 (Imaging Data & Pathways)
Chair: Zeynep Gumus
12:40 - 13:00
[proceedings talk] Metaball skinning of synthetic astroglial morphologies into realistic mesh models for in silico simulations and visual analytics
Authors: Marwan Abdellah, Alessandro Foni, Eleftherios Zisis, Nadir Roman Guerrero, Samuel Lapere, Jay S. Coggan, Daniel Keller, Henry Markram and Felix Schürmann
13:00 - 13:10
[talk] Interactive multiscale microscopy visualization on the web with Viv
Authors: Trevor Manz, Nils Gehlenborg, Mark Keller, Ilan Gold and Chuck Mccallum
13:10 - 13:30
[talk] Loon: Using Exemplars to Visualize Large Scale Microscopy Data
Authors: Devin Lange, Eddie Polanco, Robert Judson-Torres, Thomas Zangle and Alexander Lex
13:30 - 13:50
[talk] ShapoGraphy: a glyph-oriented visualisation approach for creating pictorial representations of bioimaging data
Authors: Heba Sailem
13:50 - 14:00
[talk] An Extensive Visualization Suite for Pathway/Genome Databases
Authors: Peter Karp and Suzanne Paley

14:20 - 15:20
July 27: BioVis Keynote and Closing
Chair: Michael Krone & Cagatay Turkay
14:20 - 15:10
[keynote] BioVis Keynote: Theories of inference for visualization interactions
Authors: Jessica Hullman
15:10 - 15:20
BioVis Award Ceremony & Closing
Speaker: Michael Krone & Cagatay Turkay

Accepted Posters (15:20 - 16:20 both days)
[poster] CooPer plots - the next level of UpSet plots
Authors: Sarah Sandmann, Martin Dugas and Julian Varghese
[poster] ShapoGraphy: a glyph-oriented visualisation approach for creating pictorial representations of bioimaging data
Authors: Heba Sailem
[poster] Vesalius: Image-free extraction and analysis of tissue anatomy by using image processing applied to sequencing base Spatial Transcriptomics
Authors: Patrick Martin
[poster] Color encoding of high-dimensional data using the CIELAB color space and state-of-the-art dimensionality reduction techniques
Authors: Mikaela Koutrouli, John H. Morris and Lars J. Jensen
[poster] SARS-CoV-2 variant timemaps
Authors: Rene Warren and Inanc Birol
[poster] Hierarchical interactive exploration and analysis of single cell RNA-seq datasets
Authors: Jayaram Kancherla, Kazi Tasnim Zinat, Stephanie Hicks and Hector Corrada Bravo
[poster] TranScape VR – A tool for visualizing transcriptomic landscapes in Virtual Reality
Authors: Annika Kreikenbohm and Anda Iosip
[poster] Visualisation of Identical-By-State regions across multiple assembled genomes.
Authors: Ricardo Humberto Ramirez Gonzalez, Jemima Brinton and Cristobal Uauy
[poster] Benchmarking framework for optimal visualization and interpretability of high-dimensional separable data
Authors: Komlan Atitey and Benedict Anchang
[poster] Association Plots reveal cluster-specific genes from high-dimensional transcriptome data
Authors: Elzbieta Gralinska and Martin Vingron
[poster] OmicsTIDE: Interactive Exploration of Trends in Multi-Omics Data
Authors: Theresa Anisja Harbig, Julian Fratte, Michael Krone and Kay Nieselt
[poster] Loon: Using Exemplars to Visualize Large Scale Microscopy Data
Authors: Devin Lange, Eddie Polanco, Robert Judson-Torres, Thomas Zangle and Alexander Lex
[poster] PlaToLoCo: platform of tools for low complexity regions in proteins
Authors: Patryk Jarnot, Joanna Ziemska-Legięcka, Laszlo Dobson, Matthew Merski, Pablo Mier, Miguel Andrade-Navarro, John Hancock, Zsuzsanna Dosztányi, Lisanna Paladin, Marco Necci, Damiano Piovesan, Silvio Tosatto, Vasilis Promponas, Marcin Grynberg and Aleksandra Gruca
[poster] Visualization of SARS-CoV-2 Genome Atlas
Authors: Kavya Vaddadi, Naina Tiwari, Aditya Rao, Vangala Govindakrishnan Saipradeep, Thomas Joseph, Rajgopal Srinivasan and Naveen Sivadasan
[poster] A look at trails through the pangenome visualization jungle
Authors: Éloi Durant, Francois Sabot, Matthieu Conte and Mathieu Rouard
[poster] A Multi-scale Approach for Biological Graph Visualization: Local Analysis in Global Context
Authors: Fahd Husain, Rosa Romero Gomez, Dario Segura, Adamo Carolli, Lai Chung Liu, Manfred Cheung and Yohann Paris
[poster] Grammar-Based Interactive Visualization of Genomics Data
Authors: Sehi L'Yi, Qianwen Wang, Fritz Lekschas and Nils Gehlenborg
[poster] An Extensive Visualization Suite for Pathway/Genome Databases
Authors: Peter Karp and Suzanne Paley
[poster] Interactive multiscale microscopy visualization on the web with Viv
Authors: Trevor Manz, Nils Gehlenborg, Mark Keller, Ilan Gold and Chuck Mccallum
[poster] State-based Visual Analysis of Disease Progression with ThreadStates
Authors: Qianwen Wang, Tali Mazor, Theresa Anisja Harbig, Ethan Cerami and Nils Gehlenborg
[poster] Python and R packages for Interactive Visualization of Spatial Single-Cell Omics Data
Authors: Mark Keller, Trevor Manz, Tessa Han, Ilan Gold, Chuck McCallum and Nils Gehlenborg
[poster] Explaining Deep Learning Approaches in Drug Repurposing through Interactive Data Visualization
Authors: Qianwen Wang, Kexin Huang, Payal Chandak, Marinka Zitnik and Nils Gehlenborg
[poster] PhosProViz: A web-based tool to generate, explore, and share interactive phosphoproteomics networks
Authors: Shreya Chandrasekar, Irene Font Peradejordi, Berk Turhan, Selim Kalayci, Jeffrey Johnson and Zeynep H. Gümüş
[poster] Lower Dimensional Representation for Spatial Transcriptomics Data in Hyperbolic Space
Authors: Mayank Musaddi and Anant Agarwal
[poster] CovRadar: Continuously tracking and filtering SARS-CoV-2 mutations for molecular surveillance
Authors: Alice Wittig, Fábio Malcher Miranda, Martin Hölzer, Tom Altenburg, Jakub Bartoszewicz, Marius Dieckmann, Ulrich Genske, Sven Giese, Melania Nowicka, Henning Schiebenhoefer, Anna-Juliane Schmachtenberg, Ming Tang, Bernhard Renard and Stephan Fuchs