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• W2936596188 abstract "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. 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. 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." @default.
• W2936596188 created "2019-04-25" @default.
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• W2936596188 date "2019-04-15" @default.
• W2936596188 modified "2023-10-10" @default.
• W2936596188 title "Metabopolis: scalable network layout for biological pathway diagrams in urban map style" @default.
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• W2936596188 doi "https://doi.org/10.1186/s12859-019-2779-4" @default.
• W2936596188 hasPubMedCentralId "https://www.ncbi.nlm.nih.gov/pmc/articles/6466808" @default.
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• W2936596188 hasPublicationYear "2019" @default.
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