BioLayout Express3D Version 3.3 Released

Network exported to D3.js and displayed in SafariThe new Version 3.3 release of BioLayout Express3D is available now from our Download page.

We have developed a range of exciting new features, including:

  • Export of graphs to D3.js/HTML for display in a web browser
  • Enhanced Pathway Commons client – compatible with brand new Pathway Commons version 6
  • More BioPAX features displayed in Class Viewer
  • Hand gesture control of graph navigation with the LeapMotion device
  • MCL clustering upgraded to latest version

This release introduces an exporter to convert your graphs into a web-friendly format, so you can display a version of your graph on a website. The exporter may be found in the BioLayout menu under File > Export. This produces an HTML file, which contains a visualisation of your graph that uses the popular D3.js data visualisation framework. The coloured nodes in your graph representing classes are preserved (e.g. classes created from MCL clustering). D3 provides a dynamic visualisation of your graph rather than a static image. This visualisation is compatible with all modern web browsers without requiring plugins.

We have made improvements to our Pathway Commons client that was introduced in BioLayout version 3.2. Pathway Commons version 6 contains data from 12 pathway and interaction databases, including IntAct and BioGRID. Our client contains options to restrict the search to data from any of these data sources. We have removed the organism option as Pathway Commons now focuses on human data. The client displays the size value for a selected search hit, a brand new Pathway Commons feature which gives an indication of the number of interactants prior to downloading. This improves performance as previously we were calculating this measure using an additional traverse query for each search hit.

We have improved the exploration of BioPAX graphs by providing more BioPAX data fields in the Class Viewer.

This new release of BioLayout includes hand gesture control using the LeapMotion device. We have integrated the Molecular Control Toolkit into BioLayout. This system was originally developed by Kenny Sabir for Aquaria, the 3D molecular viewer developed in Seán O’Donoghue’s group at The Garvan Institute in Australia. We hope that this provides an intuitive way to interact with 3D graphs. To try this feature out, purchase an inexpensive LeapMotion device, install the LeapMotion software from, then plug the LeapMotion controller into a USB port before starting BioLayout.

We have also included the latest MCL binaries for more efficient clustering.

To learn more about how to use these these new features, read BioLayout Express3D Version 3.3 detailed Release Notes.

We are working on a new version of the manual to fully document these new features.

We would like to thank Stijn van Dongen for supplying the latest version of MCL, Kenny Sabir for support with Molecular Control Toolkit and Igor Rodchenkov for support with Pathway Commons integration.

Network viewed in BioLayout before D3.js export
Network viewed in BioLayout before D3.js export
Network exported to D3.js and displayed in Safari
Network exported to D3.js viewed in Safari