The Travel of a Metabolite

Information

• Publication Type: Miscellaneous Publication
• Workgroup(s)/Project(s):
  • BioNetIllustration: User Centric Illustrations of Biological Networks
• Date: 2018
• Note: submitted to PacificVis 2018 Data Story Telling Contest

Abstract

Biological pathways are chains of molecule interactions and reactions in biological systems that jointly form complex, hierarchical networks. Although several pathway layout algorithms have been investigated, biologists still prefer to use hand-drawn ones, due to their high visual quality relied on domain knowledge. In this project, we propose a visualization for computing metabolic pathway maps that restrict the grouping structure defined by biologists to rectangles and apply orthogonal-style edge routing to simplify edge orientation. This idea is inspired by concepts from urban planning, where we consider reactions as city blocks and built up roads to connect identical metabolites occurred in multiple categories. We provide a story to present how glucose is broken down to phosphoenolpyruvate to release energy, which is often stored in adenosine triphosphate (ATP) in a human body. Finally, we demonstrate ATP is also utilized to synthesize urea to eliminate the toxic ammonia in our body.

Additional Files and Images

Weblinks

• https://vimeo.com/258174044

BibTeX

@misc{wu-2018-story,
  title =      "The Travel of a Metabolite",
  author =     "Hsiang-Yun Wu and Martin N\"{o}llenburg and Ivan Viola",
  year =       "2018",
  abstract =   "Biological pathways are chains of molecule interactions and
               reactions in biological systems that jointly form complex,
               hierarchical networks. Although several pathway layout
               algorithms have been investigated, biologists still prefer
               to use hand-drawn ones, due to their high visual quality
               relied on domain knowledge. In this project, we propose a
               visualization for computing metabolic pathway maps that
               restrict the grouping structure defined by biologists to
               rectangles and apply orthogonal-style edge routing to
               simplify edge orientation. This idea is inspired by concepts
               from urban planning, where we consider reactions as city
               blocks and built up roads to connect identical metabolites
               occurred in multiple categories. We provide a story to
               present how glucose is broken down to phosphoenolpyruvate to
               release energy, which is often stored in adenosine
               triphosphate (ATP) in a human body. Finally, we demonstrate
               ATP is also utilized to synthesize urea to eliminate the
               toxic ammonia in our body.",
  month =      apr,
  note =       "submitted to PacificVis 2018 Data Story Telling Contest",
  URL =        "https://www.cg.tuwien.ac.at/research/publications/2018/wu-2018-story/",
}