eXpanda: An integrated platform for network analysis and visualization

Yoshiteru Negishi, Hiroyuki Nakamura, Nozomu Yachie, Rintaro Saito, Masaru Tomita

Research output: Contribution to journalArticle

4 Citations (Scopus)

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/.

Original languageEnglish
Pages (from-to)141-144
Number of pages4
JournalIn Silico Biology
Volume7
Issue number2
Publication statusPublished - 2007 Sep 4

Keywords

  • Interactome
  • Network analysis
  • Network visualization
  • Perl library
  • Scalable Vector Graphics (SVG)

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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  • Cite this

    Negishi, Y., Nakamura, H., Yachie, N., Saito, R., & Tomita, M. (2007). eXpanda: An integrated platform for network analysis and visualization. In Silico Biology, 7(2), 141-144.