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BioLayoutJava

Versatile Network Visualisation of Structural and Functional Relationships

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Applied Bioinformatics

Abstract

Visualisation of biological networks is becoming a common task for the analysis of high-throughput data. These networks correspond to a wide variety of biological relationships, such as sequence similarity, metabolic pathways, gene regulatory cascades and protein interactions. We present a general approach for the representation and analysis of networks of variable type, size and complexity. The application is based on the original BioLayout program (C-language implementation of the Fruchterman-Rheingold layout algorithm), entirely re-written in Java™ to guarantee portability across platforms. BioLayoutJava provides broader functionality, various analysis techniques, extensions for better visualisation and a new user interface. Examples of analysis of biological networks using BioLayoutJava are presented.

Availability: BioLayoutJava has been tested on Windows® XP, Mac OS® X, Linux and Solaris™ operating systems, and is available from http://www.biolayout.org. The program is free for academic and non-profit research institutions.

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Acknowledgements

We thank the Computational Genomics Group at the European Bioinformatics Institute for extensive testing and invaluable suggestions.

No sources of funding were used to assist in the preparation of this article. The authors have no conflicts of interest that are directly relevant to the Outstation, content of this article.

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Authors and Affiliations

  1. Computational Genomics Group, European Bioinformatics Institute, EMBL Cambridge Outstation, Cambridge, CB10 1SD, UK

    Leon Goldovsky, Ildefonso Cases, Anton J. Enright &  Christos A. Ouzounis

Authors
  1. Leon Goldovsky
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  2. Ildefonso Cases
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  3. Anton J. Enright
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  4. Christos A. Ouzounis
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Corresponding author

Correspondence to Christos A. Ouzounis.

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Goldovsky, L., Cases, I., Enright, A.J. et al. BioLayoutJava . Appl-Bioinformatics 4, 71–74 (2005). https://doi.org/10.2165/00822942-200504010-00009

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  • DOI: https://doi.org/10.2165/00822942-200504010-00009

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