BioNetIllustration: User Centric Illustrations of Biological Networks

General Information

In living systems, one molecule is commonly involved in several distinct physiological functions. The roles of molecules are commonly summarized in pathway diagrams, which, however, are abstract, hierarchically nested and thus is difficult to comprehend especially by non-expert audience. The primary goal of this research in visualization is to intuitively support the comprehensive understanding of relationships among biological networks using interactively computed illustrations. Illustrations, especially in textbooks of biology are carefully designed to clearly present reactions between organs as well as interactions within cells. Automatic generation of illustrative visualizations of biological networks is thus the technical content of this proposal. Automatic generation of hand-drawn illustrations has been a challenging task due to the difficulty of algorithmically describing a human creative process such as evaluating and selecting significant information and composing meaningful explanations in a visually plausible manner. The project also involves experts from several disciplines including network and medical visualization, data mining, systems biology as well as perceptual psychology. The result will provide a new direction for physiological process analysis and accelerate the knowledge transfer not only within experts but also to the public.

Publications

12 Publications found:
Image Bib Reference Publication Type
2019
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
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. September 2019.
Conference Paper
Kazuyo Mizuno, Hsiang-Yun Wu, Shigeo Takahashi, Takeo Igarashi
Optimizing Stepwise Animation in Dynamic Set Diagrams
Computer Graphics Forum, July 2019. [video]
Journal Paper with Conference Talk
Hsiang-Yun Wu, Martin Nöllenburg, Filipa L. Sousa, Ivan Viola
Metabopolis: Scalable Network Layout for Biological Pathway Diagrams in Urban Map Style
BMC Bioinformatics, (187), May 2019. [paper] [video]
Journal Paper (without talk)
Hsiang-Yun Wu, Benjamin Niedermann, Shigeo Takahashi, Martin Nöllenburg
A Survey on Computing Schematic Network Maps: The Challenge to Interactivity, 11. April 2019, The 2nd Schematic Mapping Workshop 2019, Vienna, Austria
WorkshopTalk
Vahan Yoghourdjian, Daniel Archambault, Stephan Diehl, Tim Dwyer, Karsten Klein, Helen C. Purchase, Hsiang-Yun Wu
Exploring the limits of complexity: A survey of empirical studies ongraph visualisation
Visual Informatics, (4), January 2019.
Journal Paper (without talk)
David Kouřil, Ladislav Čmolík, Barbora Kozlikova, Hsiang-Yun Wu, Graham Johnson, David Goodsell, Arthur Olson, Meister Eduard Gröller, Ivan Viola
Labels on Levels: Labeling of Multi-Scale Multi-Instance and Crowded 3D Biological Environments
IEEE Transactions on Visualization and Computer Graphics, January 2019. [LoL-conference-presentation] [paper]
Journal Paper with Conference Talk
2018
Daniel Archambault, Jessie Kennedy, Tatiana von Landesberger, Mark McCann, Fintan McGee, Benjamin Renoust, Hsiang-Yun Wu
Lost in Translation: Alignment of Mental Representations for Visual Analytics, Reimagining the Mental Map and Drawing Stability (NII Shonan Meeting Seminar 127)
, December 2018 [paper]
Technical Report
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
Hsiang-Yun Wu, Martin Nöllenburg, Ivan Viola
The Travel of a Metabolite
submitted to PacificVis 2018 Data Story Telling Contest
Miscellaneous Publication
Hsiang-Yun Wu, Shigeo Takahashi, Rie Ishida
Overlap-Free Labeling of Clustered Networks Based on Voronoi Tessellation
Journal of Visual Languages & Computing, (44), February 2018.
Journal Paper (without talk)
Radu Jianu, Martin Krzywinski, Luana Micallef, Hsiang-Yun Wu
Mapifying the Genome, Scalable Set Visualizations (Dagstuhl Seminar 17332)
, 2018 [paper]
Technical Report
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