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Link to original content: https://pubmed.ncbi.nlm.nih.gov/20460470/
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. 2010 Jul;38(Web Server issue):W150-4.
doi: 10.1093/nar/gkq352. Epub 2010 May 11.

VISIBIOweb: visualization and layout services for BioPAX pathway models

Alptug Dilek  1 , Mehmet E Belviranli, Ugur Dogrusoz
Affiliations

VISIBIOweb: visualization and layout services for BioPAX pathway models

Alptug Dilek et al. Nucleic Acids Res. 2010 Jul.

Abstract

With recent advancements in techniques for cellular data acquisition, information on cellular processes has been increasing at a dramatic rate. Visualization is critical to analyzing and interpreting complex information; representing cellular processes or pathways is no exception. VISIBIOweb is a free, open-source, web-based pathway visualization and layout service for pathway models in BioPAX format. With VISIBIOweb, one can obtain well-laid-out views of pathway models using the standard notation of the Systems Biology Graphical Notation (SBGN), and can embed such views within one's web pages as desired. Pathway views may be navigated using zoom and scroll tools; pathway object properties, including any external database references available in the data, may be inspected interactively. The automatic layout component of VISIBIOweb may also be accessed programmatically from other tools using Hypertext Transfer Protocol (HTTP). The web site is free and open to all users and there is no login requirement. It is available at: http://visibioweb.patika.org.

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Figures

Figure 1.
Figure 1.
High-level architecture of VISIBIOweb depicted with a UML component diagram.
Figure 2.
Figure 2.
A sample screenshot from VISIBIOweb. The GUI is organized into a menu bar, a toolbar, and a canvas with various controls. An object inspection window is opened upon demand.
Figure 3.
Figure 3.
Display and layout options in load dialog.
Figure 4.
Figure 4.
A sample view of the Persist BioPAX model view dialog.
Figure 5.
Figure 5.
A sample pathway view (Cam-PDE 1 activation) and its geometry in native VISIBIOweb format (certain parts hidden for brevity).
See this image and copyright information in PMC

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