Get Started

We aim to make BioLayout Express3D easy to deploy and a joy for anyone to use. For this reason it has been designed to work on all standard computing platforms (Windows 32/64bit, MacOSX, Linux 32/64bit) and to make best use of the available hardware. We are also continuously pushing the boundaries of what is possible in the rendering of large network graphs, and looking to make the program faster and more powerful. Balancing the two objectives is not easy and we expend a considerable amount of effort to try and ensure that the program is compatible with all computing set ups. However, predicting how the program will work on all computing platforms, configurations and driver installations is impossible.

Get BioLayout Express3D

  • Download the installer package for Windows or Mac and run the installer.
  • For Linux, download the universal JAR file (does not require installation).
  • Alternatively run the Web Start automatic online deployment process (Windows/Mac/Linux), available from the BioLayout Express3D website. Click the “LAUNCH” button in the right-hand sidebar. This opens the application with a preloaded expression dataset.

It is recommended that you start by opening some of the example graphs available under the datasets page of the website. Start with small graphs and build up from there in order to test your hardware/software configuration and its ability to render large graphs. If these run you will likely be OK with graphs of your own making. If your graphs do not work the most likely explanation is that the input format is incorrect (see below) or you may need to upgrade your OpenGL drivers. If the application does not run please check the system requirements section and if still no explanation, e-mail support@biolayout.org.

Graph Navigation

Using the 3D Interface

Visualization of networks in 3-dimensions provides a fast and powerful interface to understand the often complex relationships between the entities represented in the graph. To interact with 3D graphs:

  • Left mouse button for rotation of the current view.
  • Middle mouse button for sideways movement (translation) of the current view.
  • Right mouse button for zoom in/out.
  • Holding down Shift + Click the left mouse button on a node selects it and makes it the centre of the graph.
  • Holding down Shift while dragging the left mouse button is used to select nodes in the graph.
  • Holding down Shift + Alt while dragging the left mouse button is used to select even more nodes in the graph, without deselecting the previous ones.

These commands are also available under the 3D menu bar.

Using the 2D Interface

To interact with 2D graphs:

  • Left mouse button for moving around the current view (translation).
  • Right mouse button for zoom in/out.
  • Holding down Alt + Click the left mouse button on a node selects it and makes it the centre of the graph (when at default view only).
  • Holding down Shift while dragging the left mouse button is used to select nodes in the graph.
  • Holding down Shift + Alt while dragging the left mouse button is used to select even more nodes in the graph, without deselecting the previous ones.

These commands are also available under the 2D menu bar.