Genome dashboards: Framework and Examples

Abstract

Genomics is a sequence-based informatics science and a 3D structure-based material science. Here we describe a framework for developing genome dashboards specifically designed to unify informatics with studies of chromatin structure and dynamics. The framework is based on the mathematical representation of geometrically exact rod models and the generalization of DNA base pair step parameters. A Model-View-Controller software design approach is proposed to implement genome dashboards as finite state machines either as desktop or web based applications. Two examples are demonstrated using our minimal genome dashboard called G-Dash-min. The data unification achieved with a genome dashboard supports the bi-directional exchange of data between informatics and structure. Thus any experimentally or theoretically determined sequence based informatics track can inform DNA, nucleosome or chromatin modeling (e.g. nucleosome positions) and structure features can be analyzed as informatics tracks in a genome browser (e.g. DNA base pair step parameters: Roll, Tilt, Twist). Here the framework is applied to chromatin, but genome dashboards are more broadly applicable. Genome dashboards are a novel means of investigating structure-function relationships for regions of the genome ranging from base pairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.