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

Fingerprint

Network Analysis
Electric network analysis
Visualization
Biological Networks
Proteins
Protein
Software
Living Systems
Graph theory
Licensure
Software Package
Software packages
Documentation
Libraries
DNA
Topology
Databases
Unit
Interaction
Range of data

Keywords

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

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

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.

eXpanda : An integrated platform for network analysis and visualization. / Negishi, Yoshiteru; Nakamura, Hiroyuki; Yachie, Nozomu; Saito, Rintaro; Tomita, Masaru.

In: In Silico Biology, Vol. 7, No. 2, 2007, p. 141-144.

Research output: Contribution to journalArticle

Negishi, Y, Nakamura, H, Yachie, N, Saito, R & Tomita, M 2007, 'eXpanda: An integrated platform for network analysis and visualization', In Silico Biology, vol. 7, no. 2, pp. 141-144.
Negishi, Yoshiteru ; Nakamura, Hiroyuki ; Yachie, Nozomu ; Saito, Rintaro ; Tomita, Masaru. / eXpanda : An integrated platform for network analysis and visualization. In: In Silico Biology. 2007 ; Vol. 7, No. 2. pp. 141-144.
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