BioJS: an open source standard for biological visualisation - its status in 2014

Abstract

BioJS is a community-based standard and repository of functional components to represent biological information on the web. The development of BioJS has been prompted by the growing need for bioinformatics visualisation tools to be easily shared, reused and discovered. Its modular architecture makes it easy for users to find a specific functionality without needing to know how it has been built, while components can be extended or created for implementing new functionality. The BioJS community of developers currently provides a range of functionality that is open access and freely available. A registry has been set up that categorises and provides installation instructions and testing facilities at http://www.ebi.ac.uk/tools/biojs/. The source code for all components is available for ready use at https://github.com/biojs/biojs.

Figure 1.

1a shows the different layers that a BioJS component is divided into. The representation layer sits on top of the JavaScript layer, which similarly possesses a layer of dependencies and a style. 1b presents an example of interactivity between three components, a protein-protein interaction network viewer, a secondary structure viewer and a tertiary structure viewer. Proteins in the network are represented as nodes and their interactions as edges. Clicking on a node makes the secondary and tertiary structure viewers retrieve the same protein. It is possible to select a secondary structure element in the 2D viewer and see where it is located in the 3D visualisation component.

Figure 2.. Screenshot of the ExpressionAtlasBaselineSummary component page in the BioJS registry, the Expression Atlas component for displaying baseline expression of genes based on RNA-seq experiments in the Expression Atlas database.

Shown here is the transcription profiling by high throughput sequencing of RNA from individual and a mixture of 16 types of human tissues (E-MTAB-513 – Illumina Body Map). By default the ‘Overview’ tab is selected when accessing a registry component. On the right hand panel the prospective developer can test the main event functions (e.g., onError) and methods (e.g., setQuery). Dependencies are also shown. The installation tab provides the snippets of code required to install the component. Just copying and pasting this code should be sufficient for the component to work. The remaining tabs provide a more detailed explanation on the different options, methods and events specified for this component’s usage.