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

Authors:
Filipa L Sousa
Filipa L Sousa
Institute of Molecular Evolution
Germany
Ivan Viola
Ivan Viola
University of Bergen

BMC Bioinformatics 2019 Apr 15;20(1):187. Epub 2019 Apr 15.

Research Division of Computer Graphics, Institute of Visual Computing and Human- Centered Technology, TU Wien, Vienna, Austria.

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.

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Source
http://dx.doi.org/10.1186/s12859-019-2779-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6466808PMC
April 2019
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References

(Supplied by CrossRef)
Article in Nature
D Wu et al.
Nature 2018
Article in BMC Bioinformatics
P Murray et al.
BMC Bioinformatics 2017
Article in Nucleic Acids Res
M Kanehisa et al.
Nucleic Acids Res 2000
Article in Bioinformatics
A Noronha et al.
Bioinformatics 2017
Article in Nat Biotechnol
I Thiele et al.
Nat Biotechnol 2013
Article in Nucleic Acids Res
T Kelder et al.
Nucleic Acids Res 2012
Article in Nucleic Acids Res
M Kutmon et al.
Nucleic Acids Res 2016
Article in Nucleic Acids Res
A Chang et al.
Nucleic Acids Res 2018
Article in Nucleic Acids Res
S Placzek et al.
Nucleic Acids Res 2017
Article in Bioinformatics
K Sidiropoulos et al.
Bioinformatics 2017

C Dunne et al.
2013

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