Genome Dashboards: Framework and Examples.

Genome Dashboards: Framework and Examples.
Biophys J. 2020 Feb 29;:
Authors: Li Z, Sun R, Bishop TC
Abstract
Genomics is a sequence-based informatics science and a three-dimensional-structure-based material science. However, in practice, most genomics researchers utilize sequence-based informatics approaches or three-dimensional-structure-based material science techniques, not both. This division is, at least in part, the result of historical developments rather than a fundamental necessity. The underlying computational tools, experimental techniques, and theoretical models were developed independently. The primary result presented here is a framework for the unification of informatics- and physics-based data associated with DNA, nucleosomes, and chromatin. The framework is based on the mathematical representation of geometrically exact rods and the generalization of DNA basepair step parameters. Data unification enables researchers to integrate computational, experimental, and theoretical approaches for the study of chromatin biology. The framework can be implemented using model-view-controller design principles, existing genome browsers, and existing molecular visualization tools. We developed a minimal, web-based genome dashboard, G-Dash-min, and applied it to two simple examples to demonstrate the usefulness of data unification and proof of concept. Genome dashboards developed using the framework and design principles presented h...

Source: Biophysical Journal - February 28, 2020 Category: Physics Authors: Li Z, Sun R, Bishop TC Tags: Biophys J Source Type: research