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Updated: Jun 13, 2026

A Web Tool for Generating High Quality Machine-readable Biological Pathways
08:01

A Web Tool for Generating High Quality Machine-readable Biological Pathways

Published on: February 8, 2017

VISIBIOweb: visualization and layout services for BioPAX pathway models.

Alptug Dilek1, Mehmet E Belviranli, Ugur Dogrusoz

  • 1Center for Bioinformatics and Computer Engineering Department, Bilkent University, Ankara 06800, Turkey.

Nucleic Acids Research
|May 13, 2010
PubMed
Summary
This summary is machine-generated.

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VISIBIOweb offers a free, open-source service for visualizing biological pathways from BioPAX data using Systems Biology Graphical Notation. This tool aids in analyzing complex cellular information and can be integrated into web pages.

Area of Science:

  • Systems Biology
  • Bioinformatics
  • Computational Biology

Background:

  • Increasing cellular data necessitates effective visualization tools for complex biological pathways.
  • Current methods for pathway representation require efficient and standardized visualization approaches.

Purpose of the Study:

  • To introduce VISIBIOweb, a web-based service for visualizing and laying out biological pathway models.
  • To provide a tool that uses Systems Biology Graphical Notation (SBGN) for clear pathway representation.
  • To enable interactive exploration and programmatic access to pathway visualizations.

Main Methods:

  • Development of a free, open-source, web-based service (VISIBIOweb).
  • Utilizes BioPAX format for pathway models.
  • Implements Systems Biology Graphical Notation (SBGN) for visualization.

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  • Offers interactive navigation (zoom, scroll) and property inspection.
  • Provides programmatic access via HTTP for the automatic layout component.

    • Main Results:

    • VISIBIOweb generates well-laid-out pathway views in SBGN format.
    • Users can embed these visualizations into their web pages.
    • Interactive features allow detailed inspection of pathway components and external database links.
    • The automatic layout functionality is accessible programmatically.

    Conclusions:

    • VISIBIOweb provides a valuable, accessible resource for visualizing and analyzing biological pathways.
    • The service simplifies the interpretation of complex cellular processes through standardized graphical notation.
    • Its web-based nature and open-source availability promote widespread adoption in biological research.