Rapid Development and Distribution of Statistical Tools for High-Throughput Sequencing Data

WP8: Advanced Data Visualisation along Genomic Coordinates

The linear sequence of chromosomes is one of the most important coordinate systems in biology, and accordingly, many visualisations of HTS data and derived results are made in the form of so-called tracks. Popular examples for this visualisation paradigm include the Ensembl and UCSC genome browsers, the Integrated Genome Browser (IGB, http://bioviz.org/igb), jbrowse (http://jbrowse.org and dalliance (http://www.biodalliance.org). To plot quantitative data (e. g., a methylation level, or a read alignment density from an RNA-Seq experiment), these tools commonly use, for each track, a line or a set of vertical bars, whose height indicates the value of the scalar signal along that track. Such displays, however, become crowded when more than a few tracks need to be visualised simultaneously.
The aim of this work package is to develop a portable, flexible, interoperable graphical browser that makes it easy to display other types of visualisations for multivariate data – in particular, heatmaps – along genomic coordinates. As the computational engine for data preparation for plotting, any R/Bioconductor component can be used, whether developed in this project or elsewhere. For the graphics layout and rendering, we will develop in two directions: using R graphics, and using HTML5/ECMAScript/SVG/Canvas based graphics libraries.
We will apply best practices in software design, engineering and testing to develop the graphical browser and the other components. We will adopt current web technology standards (HTML5, AJAX), adhere to bioinformatic data exchange protocols such as DAS and employ modern object-oriented and scripting languages (Java, ECMAScript, R) in a combination that optimizes over development time, leveraging of existing components and maintainability. Particular focus will be dedicated to the efficiency of the rendering algorithms, to careful memory management, and to asynchronous remote calls, in order to provide software which will be powerful but also efficient.


Genomnia (Lead Partner)

WP8 Genome Browser