Tool: Biolayout Express3D Version 3.1 Released
gravatar for derek.w.wright
5.6 years ago by
University of Glasgow
derek.w.wright10 wrote:

The BioLayout team is pleased to announce the release of BioLayout Express3D version 3.1, a powerful tool for the visualization and analysis of network graphs. BioLayout Express3D has been designed for visualization, clustering, exploration and analysis of very large network graphs in 3D or 2D. The software can enable a scientist to visualize biological data such as sequence similarity, metabolic pathways, protein interactions, pathways, regulatory cascades and gene expression.

Installers are available from our Download page.

The software includes a range of new features, the main ones of which are listed below:

  • Integration of the Fast Multipole Multilevel Method (FMMM) graph layout algorithm. This is a force-directed layout algorithm that allows graph layout to be computed with a small number of iterations. In practise, this produces better laid out graphs, with more sparsely arranged nodes. The algorithm is particularly useful for the
    visualisation of large datasets that BioLayout excels in.
  • All plots now use JFreeChart enabling some customisation of plots including ability to display the mean, standard deviation, standard error or interquartile range (IQR)
  • Data series can now be plotted as lines or histogram style
  • Options to filter by input value or coefficient of variation
  • Support for import of Graph Modelling Language (GML) files. GML is a popular standard file format for the exchange of graphs and is supported by a wide range of graph drawing and network visualisation software packages.

See for more information.

We would be delighted to offer support or consider any feedback or feature requests. Contact us at

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