Biological Data Visualization

In modern biological research domain experts have to deal with complex and large data collections and simulations. Our goal is to support biological researches in molecular biology and phenotyping communities by developing visualizations that complement statistical methodology and wet lab with visual data analysis. Our tools allow the domain experts to see the key information they are looking for that relates to the studied structure, such as tunnels in molecules on the nanoscale or root shape distributions on the macroscopic magnification levels. Equally important is the role of visualization in explaining certain phenomenon to a larger audience. Biologists create large structural models that reflect the state-of-the-art knowledge about a certain living organism. This form of captured knowledge can be effectively communicated with interactive visualization, especially the aspect of understanding interplay of multiple spatial and temporal scales. With our visualization technology audience can therefore seamlessly zoom from zoom level when seeing entire bacteria down to its atomic detail.

Publications

83 Publications found:
Image Bib Reference Publication Type
2020
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Multi-level Area Balancing of Clustered Graphs
IEEE Transactions on Visualization and Computer Graphics (TVCG), x:1-15, December 2020. [paper] [video]
Journal Paper (without talk)
Ladislav Čmolík, Václav Pavlovec, Hsiang-Yun Wu, Martin Nöllenburg
Mixed Labeling: Integrating Internal and External Labels
IEEE Transactions on Visualization and Computer Graphics (TVCG), x:1-14, November 2020. [image] [paper]
Journal Paper (without talk)
Elisa De Llano, Haichao Miao, Yasaman Ahmadi, Armanda J Wilson, Morgan Beeby, Ivan Viola, Ivan Barisic
Adenita: interactive 3D modelling and visualization of DNA nanostructures
Nucleic Acids Research, July 2020.
Journal Paper (without talk)
Renata Raidou, Barbora Kozlikova, Johanna Beyer, Timo Ropinski, Issei Fujishiro
NII Shonan Meeting Report No. 167: Formalizing Biological and Medical Visualization
ISSN 2186-7437
Miscellaneous Publication
Sarkis Halladjian, Haichao Miao, David Kouřil, Meister Eduard Gröller, Ivan Viola, Tobias Isenberg
ScaleTrotter: Illustrative Visual Travels Across Negative Scales
IEEE Transactions on Visualization and Computer Graphics, 26(1), January 2020. [paper]
Journal Paper with Conference Talk
Ngan Nguyen, Ondrej Strnad, Tobias Klein, Ruwayda Alharbi, Peter Wonka, Martina Maritan, Peter Mindek, Ludovic Autin, David Goodsell, Ivan Viola
Modeling in the Time of COVID-19: Statistical and Rule-based Mesoscale Models
IEEE Transactions on Visualization and Computer Graphics, 2020.
Journal Paper with Conference Talk
2019
Tobias Klein
Instant Construction of Atomistic Models for Visualization in Integrative Cell Biology
Supervisor: Ivan Viola
Duration: 2016-2019
[image]
PhD-Thesis
Tobias Klein, Peter Mindek, Ludovic Autin, David Goodsell, Arthur Olson, Meister Eduard Gröller, Ivan Viola
Parallel Generation and Visualization of Bacterial Genome Structures
Computer Graphics Forum, 38(7):57-68, November 2019.
Journal Paper with Conference Talk
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Graph Models for Biological Pathway Visualization: State of the Art and Future Challenges, 20. October 2019, Vis 2019 Workshop, Canada
[paper]
WorkshopTalk
Susanne Rinortner
Visualizing Protein Interactions in Corresponding Compartments
Bachelor Thesis
Aleksandr Amirkhanov, Ilona Kosiuk, Peter Szmolyan, Artem Amirkhanov, Gabriel Mistelbauer, Meister Eduard Gröller, Renata Raidou
ManyLands: A Journey Across 4D Phase Space of Trajectories
Computer Graphics Forum, 38(7):191-202, October 2019. [Paper] [Video demo]
Journal Paper with Conference Talk
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
Map of Metabolic Harmony
[image-full]
Unknown Publication
Maximillian Sbardellati, Haichao Miao, Hsiang-Yun Wu, Meister Eduard Gröller, Ivan Barisic, Ivan Viola
Interactive Exploded Views for Molecular Structures
In Proceedings of the 9th Eurographics Workshop on Visual Computing for Biology and Medicine, pages 103-112. September 2019.
[paper]
Conference Paper
Haichao Miao
Geometric Abstraction for Effective Visualization and Modeling
Supervisor: Ivan Viola
Duration: 90
PhD-Thesis
Tobias Klein, Ivan Viola, Meister Eduard Gröller, Peter Mindek
Multi-Scale Procedural Animations of Microtubule Dynamics Based on Measured Data
IEEE Transactions on Visualization and Computer Graphics, 26(1):622-632, August 2019. [paper]
Journal Paper with Conference Talk
Renata Raidou
Visual Analytics for the Representation, Exploration and Analysis of High-Dimensional, Multi-Faceted Medical Data
In Biomedical Visualisation, pages 137-162, July 2019
Article in a Book
Jan Byska, Thomas Trautner, Sergio Marques, Jiri Damborsky, Barbora Kozlikova, Manuela Waldner
Analysis of Long Molecular Dynamics Simulations Using Interactive Focus+Context Visualization
Computer Graphics Forum, 38(3):441-453, June 2019. [paper] [video]
Journal Paper with Conference Talk
Haichao Miao, Elisa De Llano, Ivan Viola, Ivan Barisic
Interactive Visual Analysis for the Design of DNA Nanostructures
Poster shown at NANTECH 2019 – Nucleic Acid Nanotechnology: From Algorithmic Design to Biochemical Applications – Espoo, Finland (27. May 2019-29. May 2019)
Poster
Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola
Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style
BMC Bioinformatics, 20(187):1-20, May 2019. [paper] [video]
Journal Paper (without talk)
Hsiang-Yun Wu, Haichao Miao, Ivan Viola
From Cells to Atoms - Biological Information Visualization (in Chinese)
TR-193-02-2019-1, March 2019 [paper]
Technical Report
Nicholas Waldin, Manuela Waldner, Mathieu Le Muzic, Meister Eduard Gröller, David Goodsell, Ludovic Autin, Arthur Olson, Ivan Viola
Cuttlefish: Color Mapping for Dynamic Multi‐Scale Visualizations
Computer Graphics Forum, 38(6):150-164, March 2019. [Open Access Article in Wiley Online Library]
Journal Paper (without talk)
Felix Kugler
Profiling and Optimization of Large Biomolecular Scenes
[image] [thesis]
Bachelor Thesis
Katharina Unger
Visual Comparison of Organism-Specific Metabolic Pathways
[CESCG paper]
Student Project
Johannes Weissenböck, Bernhard Fröhler, Meister Eduard Gröller, Johann Kastner, Christoph Heinzl
Dynamic Volume Lines: Visual Comparison of 3D Volumes through Space-filling Curves
IEEE TRANSACTIONS ON VISUALIZATION AND COMPUTER GRAPHICS, 25(1):1040-1049, January 2019. [image]
Journal Paper (without talk)
Haichao Miao, Tobias Klein, David Kouřil, Peter Mindek, Karsten Schatz, Meister Eduard Gröller, Barbora Kozlikova, Tobias Isenberg, Ivan Viola
Multiscale Molecular Visualization
Journal of Molecular Biology, 6(31):1049-1070, January 2019. [Paper]
Journal Paper (without talk)
Aleksandr Amirkhanov, Ilona Kosiuk, Peter Szmolyan, Artem Amirkhanov, Gabriel Mistelbauer, Meister Eduard Gröller, Renata Raidou
EG VCBM 2019 Image Contest Award, people's choice—ManyLands: A Journey Across 4D Phase Space of Biological Systems
Unknown Publication
2018
Peter Mindek
Molecular Visualization, 10. November 2018, FYI: Informationsdesign Konferenz Wien, Nordbahn-Halle, Vienna
WorkshopTalk
Maximillian Sbardellati
Interactive Exploded Views for Presenting DNA Nano-Structures
[image]
Bachelor Thesis
Thomas Trautner
Importance-Driven Exploration of Molecular Dynamics Simulations
[image] [Poster]
Master Thesis
Nicolas Grossmann, Thomas Köppel, Meister Eduard Gröller, Renata Raidou
VisualFlatter - Visual Analysis of Distortions in the Projection of Biomedical Structures
Eurographics Proceedings, September 2018.
Journal Paper with Conference Talk
Elisa De Llano, Haichao Miao, Tobias Isenberg, Meister Eduard Gröller, Ivan Viola, Ivan Barisic
A Preview to Adenita: Visualization and Modeling of DNA Nanostructures
Poster shown at 3rd Functional DNA Nanotechnology Workshop ( 6. June 2018- 8. June 2018)
Poster
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
A Visual Comparison of Hand-Drawn and Machine-Generated Human Metabolic Pathways
Poster shown at EuroVis ( 4. June 2018- 8. June 2018)
[poster]
Poster
Haichao Miao, Elisa De Llano, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola
DimSUM: Dimension and Scale Unifying Maps for Visual Abstraction of DNA Origami Structures
Computer Graphics Forum, 37(3), June 2018. [Paper]
Journal Paper with Conference Talk
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
The Travel of a Metabolite
submitted to PacificVis 2018 Data Story Telling Contest
[paper] [video]
Miscellaneous Publication
Katarína Furmanová, Jan Byska, Meister Eduard Gröller, Ivan Viola, Jan J. Paleček, Barbora Kozlikova
COZOID: contact zone identifier for visual analysis of protein-protein interactions
BMC Bioinformatics, (19:125 ):1-25, April 2018. [image] [Paper]
Journal Paper (without talk)
Thomas Koch
Semantic Screen-Space Occlusion for Multiscale Molecular Visualization
[image]
Bachelor Thesis
Lukas Lipp
Visualization of Fiber Orientation in Glass Fiber Reinforced Polymers
[Bachelor Thesis] [image]
Bachelor Thesis
Haichao Miao, Elisa De Llano, Johannes Sorger, Yasaman Ahmadi, Tadija Kekic, Tobias Isenberg, Meister Eduard Gröller, Ivan Barisic, Ivan Viola
Multiscale Visualization and Scale-adaptive Modification of DNA Nanostructures
IEEE Transactions on Visualization and Computer Graphics, 24(1), January 2018. [paper]
Journal Paper with Conference Talk
Julian Strohmayer
A Visual Analytics Approach to Hypocotyl/Root Transition Detection in Arabidopsis Thaliana
[image]
Bachelor Thesis
Tobias Klein, Ludovic Autin, Barbora Kozlikova, David Goodsell, Arthur Olson, Meister Eduard Gröller, Ivan Viola
Instant Construction and Visualization of Crowded Biological Environments
IEEE Transactions on Visualization and Computer Graphics, 2018. [paper]
Journal Paper with Conference Talk
Radu Jianu, Martin Krzywinski, Luana Micallef, Hsiang-Yun Wu
Mapifying the Genome, Scalable Set Visualizations (Dagstuhl Seminar 17332)
TR-193-02-2018-2, 2018 [paper]
Technical Report
Stefan Dietrich
Smart Visibility Technique for Linear and Planar Molecular Assemblies
Bachelor Thesis
2017
Johannes Sorger
Integration Strategies in the Visualization of Multifaceted Spatial Data
Supervisor: Ivan Viola
Duration: 2013 - 2017
[thesis]
PhD-Thesis
Stefan Dietrich
SirTom - Structural information retaining Triangle-based Occlusion Management
[Bachelor Thesis] [image]
Bachelor Thesis
Stefan Stappen
Hybrid Frames - Animated Narrative Sequences in Molecular Visualization
[teaser] [thesis]
Bachelor Thesis
Guillermo Garcia-Escribano
Visual Evaluation of Computational Models of the Biological Mesoscale
Bachelor Thesis
David Kouřil, Mathieu Le Muzic, Barbora Kozlikova, Ivan Viola
Maya2cellVIEW: Integrated Tool for Creating Large and Complex Molecular Scenes
Poster shown at Spring Conference on Computer Graphics 2017 (May 2017)
Poster
Johannes Sorger, Peter Mindek, Peter Rautek, Meister Eduard Gröller, Graham Johnson, Ivan Viola
Metamorphers: Storytelling Templates For Illustrative Animated Transitions in Molecular Visualization
In Proceedings of the Spring Conference on Computer Graphics 2017, pages 27-36. May 2017.
[paper] [teaser] [video]
Conference Paper
Daniel Gehrer, Ivan Viola
Visualization of molecular machinery using agent-based animation
In Proceedings of SCCG 2017. May 2017.
[paper]
Conference Paper
Daniel Gehrer
Visualization of molecular machinery using agent-based animation
[image] [Master thesis]
Master Thesis
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