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Tools for visually exploring biological networks.

Matthew Suderman¹, Michael Hallett

¹McGill Centre for Bioinformatics, 3775 University Street, Montreal, QCH3A 2B4, Canada. msuder@mcb.mcgill.ca

Bioinformatics (Oxford, England)

|August 28, 2007

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This review compares over 35 biological network visualization tools, aiding researchers in selecting appropriate systems for systems biology and bioinformatics. It also outlines future directions for next-generation visualization tools.

Area of Science:

Integrative biology
Systems biology
Integrative bioinformatics

Background:

Numerous tools exist for biological network visualization, including Cytoscape, VisANT, Pathway Studio, and Patika.
These tools are crucial for advancing integrative biology, systems biology, and bioinformatics.

Purpose of the Study:

To review existing biological network visualization tools, detailing their advantages and disadvantages.
To assist researchers in identifying suitable tools for their data visualization needs.
To define realistic goals for the development of next-generation visualization systems.

Main Methods:

A comprehensive review of existing biological network visualization tools.
Systematic comparison of over 35 tools based on more than 25 features (detailed in Supplementary Material).

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Main Results:

The study provides a detailed comparison of the strengths and weaknesses of current visualization tools.
A systematic comparison table of over 35 tools and 25 features is available in the Supplementary Material.

Conclusions:

Researchers can use this review and comparison to efficiently select appropriate biological network visualization tools.
The findings inform the development of future visualization systems that incorporate dynamic modeling and diverse data types.