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dc.contributor.authorWu, Hsiang-Yun
dc.contributor.authorNöllenburg, Martin
dc.contributor.authorSousa, Filipa L.
dc.contributor.authorViola, Ivan
dc.date.accessioned2019-04-22T06:17:20Z
dc.date.available2019-04-22T06:17:20Z
dc.date.issued2019-04-15
dc.identifier.citationWu H-Y, Nöllenburg M, Sousa FL, Viola I (2019) Metabopolis: scalable network layout for biological pathway diagrams in urban map style. BMC Bioinformatics 20. Available: http://dx.doi.org/10.1186/s12859-019-2779-4.
dc.identifier.issn1471-2105
dc.identifier.doi10.1186/s12859-019-2779-4
dc.identifier.urihttp://hdl.handle.net/10754/631962
dc.description.abstractBackground 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.
dc.description.sponsorshipThe authors would like to thank the members from KEGG [3], ReconMap [4], and CellDesigner [22] who have provided valuable comments to our system. The project leading to this submission has received funding from the European Union Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No. 747985, from the Vienna Science and Technology Fund (WWTF) through projects VRG11-010 and VRG15-007, from the Austrian Science Fund (FWF) through project P31119, and from King Abdullah University of Science and Technology (KAUST) through award BAS/1/1680-01-01.
dc.language.isoen
dc.publisherSpringer Nature
dc.relation.urlhttps://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-2779-4
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectBiological pathways
dc.subjectGraph drawing
dc.subjectMap metaphor
dc.subjectOrthogonal layout
dc.subjectFloor planning
dc.subjectEdge routing
dc.titleMetabopolis: scalable network layout for biological pathway diagrams in urban map style
dc.typeArticle
dc.contributor.departmentComputer Science Program
dc.contributor.departmentComputer, Electrical and Mathematical Sciences and Engineering (CEMSE) Division
dc.contributor.departmentVisual Computing Center (VCC)
dc.identifier.journalBMC Bioinformatics
dc.eprint.versionPublisher's Version/PDF
dc.contributor.institutionResearch Division of Computer Graphics, Institute of Visual Computing and Human- Centered Technology, TU Wien, Vienna, Austria.
dc.contributor.institutionAlgorithms and Complexity Group, Institute of Logic and Computation, TU Wien, Vienna, Austria.
dc.contributor.institutionArchaea Biology and Ecogenomics Division, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria.
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)
pubs.publication-statusPublished
kaust.personViola, Ivan
kaust.grant.numberBAS/1/1680-01-01
dc.relation.issupplementedbyDOI:10.6084/m9.figshare.c.4473824.v1
dc.relation.issupplementedbygithub:yun-vis/Metabopolis
refterms.dateFOA2019-04-22T06:17:21Z
display.relations<b>Is Supplemented By:</b><br/> <ul><li><i>[Dataset]</i> <br/> Hsiang-Yun Wu, Nรถllenburg Martin, Sousa, F., &amp; Viola, I. (2019). Metabopolis: scalable network layout for biological pathway diagrams in urban map style. Figshare. https://doi.org/10.6084/M9.FIGSHARE.C.4473824.V1. DOI: <a href="https://doi.org/10.6084/m9.figshare.c.4473824.v1" >10.6084/m9.figshare.c.4473824.v1</a> Handle: <a href="http://hdl.handle.net/10754/664627" >10754/664627</a></a></li><li><i>[Software]</i> <br/> Title: yun-vis/Metabopolis: Biological Pathway Visualization. Publication Date: 2018-08-22. github: <a href="https://github.com/yun-vis/Metabopolis" >yun-vis/Metabopolis</a> Handle: <a href="http://hdl.handle.net/10754/666971" >10754/666971</a></a></li></ul>
dc.date.published-online2019-04-15
dc.date.published-print2019-12


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This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
Except where otherwise noted, this item's license is described as This article is distributed under the terms of the Creative Commons Attribution 4.0 International License(http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver(http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.