Metabopolis: scalable network layout for biological pathway diagrams in urban map style
Type
DatasetKAUST Department
Computer, Electrical and Mathematical Sciences and Engineering (CEMSE) DivisionComputer Science Program
Visual Computing Center (VCC)
Date
2019Permanent link to this record
http://hdl.handle.net/10754/664627
Metadata
Show full item recordAbstract
Abstract 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.Citation
Hsiang-Yun Wu, Nรถllenburg Martin, Sousa, F., & 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.V1Publisher
figshareRelations
Is Supplement To:- [Article]
Wu 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.. DOI: 10.1186/s12859-019-2779-4 HANDLE: 10754/631962
ae974a485f413a2113503eed53cd6c53
10.6084/m9.figshare.c.4473824.v1