BEL Demos

Biological Networks from BEL Knowledge Bases

These examples demonstrate visualizations of causal biological networks derived from a knowledge base expressed in BEL (the Biological Expression Language, www.belportal.org). The knowledge is based on experimental findings encoded as BEL statements. Large network models are assembled from the knowledge base and the networks visualized here are selected sub-models of these large networks.

BEL Networks in 3D

In these examples, the networks are loaded in XGMML format. Layout is performed by a 3D force-directed layout engine.

Click on nodes to select. In the gray pane that is displayed, the perturb button allows you to initiate the animation of the causal flow downstream from the selected node.

Click the airplane icon to cause the camera to fly around the network.

WebGL Version

The WebGL examples work in recent versions of Chrome, Firefox, and Safari (with WebGL enabled). Requires a computer with a WebGL-compatible GPU.

HTML5 Canvas Version

The HTML5-based visualizer runs in a broad variety of modern browsers, including those on tablets and smart phones.
The WebGL-based visualizer renders proteins, protein activities, biological processes and other nodes as 3D objects. Nodes causal direction of edges connected to selected nodes.
The HTML5-based visualizer renders the same network using 2D objects and unshaded 3D objects.

BEL Networks in 2D

In these examples, the layout is constrained to a single x-y plane and the z-axis is used to express quantities assigned to nodes.

Click on nodes to select. In the gray pane that is displayed, the perturb button allows you to initiate the animation of the causal flow downstream from the selected node.

Click the airplane icon to cause the camera to fly around the network.

WebGL Version

HTML5 Canvas Version

WebGL-based visualizer
HTML5-based visualizer

BEL Networks Compared in Multiple Planes

BEL networks can be assembled from experimental findings in multiple species, where any given link in the network may be supported by knowledge from Human, Mouse, or Rat. In this visualization, the network is rendered in 3 planes, one for each species. Each edge is rendered in each plane where it has experimental support. Nodes connect between planes by "homology" pseudo-edges.

The value of this visualization is to aid in the understanding of biological mechanisms across species, a problem critical in drug development. Candidate drugs that show promising effects when tested in animals may subsequently fail in human trials, so improved methods to compare mechanisms between species can potentially help choose both therapeutic and testing strategies.

Click on nodes to select - causal flow to and from the node is animated when selected.

WebGL Multi-Plane Visualization

HTML5 Canvas Multi-Plane Visualization

Caveat:The network used in this example did not include the species information contained in the original BEL knowledge base. For the purposes of demonstration, species assignment of edges has been simulated. In upcoming work, this visualization will be used in conjunction with a BEL endpoint where queries will access species information in addition to the primary network structure.

WebGL-based visualizer
HTML5-based visualizer
Architecture