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Volume 7


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In Silico Biology 7, 0013 (2007); ©2007, Bioinformation Systems e.V.  



eXpanda: an integrated platform for network analysis and visualization

Yoshiteru Negishi1, 2, Hiyoyuki Nakamura1, 3, Nozomu Yachie1, 2, Rintaro Saito1, 3* and Masaru Tomita1, 2, 3

1 Institute for Advanced Biosciences, Keio University, Fujisawa, 252-8520, Japan
2 Bioinformatics Program, Graduate School of Media and Governance, Keio University, Fujisawa, 252-8520, Japan
3 Department of Environmental Information, Keio University, Fujisawa, 252-8520, Japan


* Corresponding author
  Email: rsaito@sfc.keio.ac.jp


Edited by E. Wingender; received November 28, 2006; revised January 20 and 26, 2007; accepted January 26, 2007; published February 15, 2007


Abstract

Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform, eXpanda, which enables an analysis of a very broad range of biological networks, with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics. eXpanda is under GNU General Public License. Software package, detailed documentations, source codes, and some sample scripts are downloadable at http://medcd.iab.keio.ac.jp/expanda/.


Keywords: interactome, network analysis, network visualization, Perl library, Scalable Vector Graphics (SVG)