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 here are extensible and customizable and are therefore more broadly applicable than the examples presented. We expect a number of purpose-specific genome dashboards to emerge as a novel means of investigating structure-function relationships for genomes that range from basepairs to entire chromosomes and for generating, validating, and testing mechanistic hypotheses.

中文翻译：

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基因组仪表板：框架和示例

基因组学是一门基于序列的信息科学和基于三维结构的材料科学。然而，在实践中，大多数基因组学研究人员使用基于序列的信息学方法或基于三维结构的材料科学技术，而不是两者兼而有之。这种分裂至少部分是历史发展的结果，而不是根本的必然。底层的计算工具、实验技术和理论模型都是独立开发的。这里介绍的主要结果是统一与 DNA、核小体和染色质相关的基于信息学和物理学的数据的框架。该框架基于几何精确杆的数学表示和 DNA 碱基对步骤参数的概括。数据统一使研究人员能够整合计算、实验和理论方法来研究染色质生物学。该框架可以使用模型-视图-控制器设计原则、现有的基因组浏览器和现有的分子可视化工具来实现。我们开发了一个基于网络的最小基因组仪表板 G-Dash-min，并将其应用于两个简单的示例，以证明数据统一和概念验证的有用性。使用此处介绍的框架和设计原则开发的基因组仪表板具有可扩展性和可定制性，因此比提供的示例具有更广泛的适用性。