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Tools for visually exploring biological networks (2007)
| Venue: | BIOINFORMATICS |
| Citations: | 57 - 0 self |
BibTeX
@ARTICLE{Suderman07toolsfor,
author = {Matthew Suderman and Michael Hallett},
title = { Tools for visually exploring biological networks},
journal = {BIOINFORMATICS},
year = {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. 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.
Keyphrases
biological network cellular process next generation relative advantage comprehensive review system biology realistic goal integrative biology dynamic model well-known example appropriate existing tool key role integrative bioinformatics gene expression data supplementary material static representation first goal many tool data visualization time-dependent behavior cellular state visualization tool pathway studio systematic comparison different feature subcellular localization information
