H. Wu, M. Nöllenburg, F. Filipa L. Sousa, I. Viola:
"Metabopolis: scalable network layout for biological pathway diagrams in urban map style";
BMC Bioinformatics, 20 (2019), 187; S. 1 - 20.

Kurzfassung englisch:
Background: Biological pathways represent chains of molecular interactions in biological systems that jointly form
complex dynamic networks. The network structure changes from the significance of biological experiments and
layout algorithms often sacrifice low-level details to maintain high-level information, which complicates the entire
image to large biochemical systems such as human metabolic pathways.
Results: Our work is inspired by concepts from urban planning since we create a visual hierarchy of biological
pathways, which is analogous to city blocks and grid-like road networks in an urban area. We automatize the manual
drawing process of biologists by first partitioning the map domain into multiple sub-blocks, and then building the
corresponding pathways by routing edges schematically, to maintain the global and local context simultaneously.
Our system incorporates constrained floor-planning and network-flow algorithms to optimize the layout of
sub-blocks and to distribute the edge density along the map domain. We have developed the approach in close
collaboration with domain experts and present their feedback on the pathway diagrams based on selected use cases.
Conclusions: We present a new approach for computing biological pathway maps that untangles visual clutter by
decomposing large networks into semantic sub-networks and bundling long edges to create space for presenting
relationships systematically.

Biological pathways, Graph drawing, Map metaphor, Orthogonal layout, Floor planning, Edge routing

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