Tools for Visually Exploring Biological Networks.

by: Matthew Suderman, Michael Hallett

Bioinformatics (25 August 2007)

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Abstract

Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond "static" representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information, and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. changeIn view of the first goal, we provide in the Supplementary Materials a systematic comparison of more than 35 existing tools in terms of over 25 different features CONTACT: msuder@mcb.mcgill.ca.

@article{citeulike:1602005, abstract = {Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond "static" representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information, and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. change{In view of the first goal, we provide in the Supplementary Materials a systematic comparison of more than 35 existing tools in terms of over 25 different features CONTACT: msuder@mcb.mcgill.ca.}}, address = {McGill Centre for Bioinformatics, 3775 University Street, Montreal, QC, Canada H3A 2B4.}, author = {Suderman, Matthew and Hallett, Michael }, citeulike-article-id = {1602005}, doi = {10.1093/bioinformatics/btm401}, issn = {1460-2059}, journal = {Bioinformatics}, month = {August}, posted-at = {2008-04-28 06:38:07}, priority = {0}, title = {Tools for Visually Exploring Biological Networks.}, url = {http://dx.doi.org/10.1093/bioinformatics/btm401}, year = {2007} }

RIS record

TY - JOUR ID - citeulike:1602005 L3 - citeulike-article-id:1602005 TI - Tools for Visually Exploring Biological Networks. JF - Bioinformatics AD - McGill Centre for Bioinformatics, 3775 University Street, Montreal, QC, Canada H3A 2B4. SN - 1460-2059 N2 - Many tools exist for visually exploring biological networks including well-known examples such as Cytoscape, VisANT, Pathway Studio and Patika. These systems play a key role in the development of integrative biology, systems biology and integrative bioinformatics. The trend in the development of these tools is to go beyond "static" representations of cellular state, towards a more dynamic model of cellular processes through the incorporation of gene expression data, subcellular localization information, and time-dependent behavior. We provide a comprehensive review of the relative advantages and disadvantages of existing systems with two goals in mind: to aid researchers in efficiently identifying the appropriate existing tools for data visualization; to describe the necessary and realistic goals for the next generation of visualization tools. change{In view of the first goal, we provide in the Supplementary Materials a systematic comparison of more than 35 existing tools in terms of over 25 different features CONTACT: msuder@mcb.mcgill.ca. AU - Suderman, Matthew AU - Hallett, Michael PY - 2007/08/25/ UR - http://dx.doi.org/10.1093/bioinformatics/btm401 ER -

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