Metabopolis: scalable network layout for biological pathway diagrams in urban map style

Autor(en)
Hsiang-Yun Wu, Martin Nöllenburg, Filipa L Sousa, Ivan Viola
Abstrakt

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.

Organisation(en)
Department für Ökogenomik und Systembiologie
Externe Organisation(en)
Technische Universität Wien, King Abdullah University for Science and Technology
Journal
BMC Bioinformatics
Band
20
Anzahl der Seiten
20
ISSN
1471-2105
DOI
https://doi.org/10.1186/s12859-019-2779-4
Publikationsdatum
04-2019
Peer-reviewed
Ja
ÖFOS 2012
Softwareentwicklung, Bioinformatik
Schlagwörter
Link zum Portal
https://ucris.univie.ac.at/portal/de/publications/metabopolis-scalable-network-layout-for-biological-pathway-diagrams-in-urban-map-style(71a7e1ff-d9a6-4df3-9ee0-8b7760ffd364).html