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Tsinghua Science and Technology 2013, 18(5): 515-521 https://doi.org/10.1109/TST.2013.6616524
Open Access | Issue | Published: 03 October 2013

Visualization of Biomolecular Networks’ Comparison on Cytoscape

Show Author's Information Jiang Xie,  Zhonghua Zhou,  Kai Lu,  Luonan Chen,  Wu Zhang( )
School of Computer Engineering and Science, Shanghai University, Shanghai 200072, China
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China
Keywords:
biomolecular networks comparison, visualization, Cytoscape
Cite this article:
Xie J, Zhou Z, Lu K, et al. Visualization of Biomolecular Networks’ Comparison on Cytoscape. Tsinghua Science and Technology, 2013, 18(5): 515-521. https://doi.org/10.1109/TST.2013.6616524
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Abstract Full text About this article

Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match (BNMatch) is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.


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About this article

Visualization of Biomolecular Networks’ Comparison on Cytoscape

Show Author's information Jiang Xie, Zhonghua Zhou, Kai Lu, Luonan Chen, Wu Zhang( )
School of Computer Engineering and Science, Shanghai University, Shanghai 200072, China
Key Laboratory of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

Abstract

Similarities and dissimilarities between biomolecular networks cannot be intuitively recognized even after the development of several comparison algorithms because of the lack of visualization tools. In this paper, an integrated tool kit named Biomolecular Network Match (BNMatch) is designed and developed based on Cytoscape—a popular and open-source tool for analyzing and visualizing networks. BNMatch integrates the comparison of the outputs of algorithms used for processing biomolecular networks and expresses the matching data between them by defining similar vertices and links with similar attributes. Moreover, in order to maintain consistency, their counterparts in other networks change when the nodes and edges in one of the compared networks are changed. It becomes easy for users to analyze similar networks by invoking comparison algorithms and visualizing the matching data between the networks using BNMatch.

Keywords: biomolecular networks comparison, visualization, Cytoscape

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Received: 06 August 2013
Revised: 20 August 2013
Accepted: 21 August 2013
Published: 03 October 2013
Issue date: October 2013

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© The author(s) 2013

Acknowledgements

The authors would like to thank Mr. Lei Yu for his participating in this work. This work was supported by Key Project of Science and Technology Commission of Shanghai Municipality (No. 11510500300) and Ph.D. Programs Fund of Ministry of Education of China (No. 20113108120022).

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