Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

James T Robinson; Douglass Turner; Neva C Durand; Helga Thorvaldsdóttir; Jill P Mesirov; Erez Lieberman Aiden

doi:10.1016/j.cels.2018.01.001

Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

Cell Syst. 2018 Feb 28;6(2):256-258.e1. doi: 10.1016/j.cels.2018.01.001. Epub 2018 Feb 7.

Authors

James T Robinson¹, Douglass Turner², Neva C Durand³, Helga Thorvaldsdóttir⁴, Jill P Mesirov⁵, Erez Lieberman Aiden⁶

Affiliations

¹ School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
² School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
³ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA.
⁵ School of Medicine, University of California San Diego, La Jolla, CA 92093, USA; Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; Moores Cancer Center, University of California San Diego, La Jolla, CA 92037, USA.
⁶ Broad Institute of MIT and Harvard, Cambridge, MA 02142, USA; The Center for Genome Architecture, Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA; Center for Theoretical Biological Physics, Rice University, Houston, TX 77030, USA; Department of Computer Science, Rice University, Houston, TX 77030, USA. Electronic address: erez@erez.com.

Abstract

Contact mapping experiments such as Hi-C explore how genomes fold in 3D. Here, we introduce Juicebox.js, a cloud-based web application for exploring the resulting datasets. Like the original Juicebox application, Juicebox.js allows users to zoom in and out of such datasets using an interface similar to Google Earth. Juicebox.js also has many features designed to facilitate data reproducibility and sharing. Furthermore, Juicebox.js encodes the exact state of the browser in a shareable URL. Creating a public browser for a new Hi-C dataset does not require coding and can be accomplished in under a minute. The web app also makes it possible to create interactive figures online that can complement or replace ordinary journal figures. When combined with Juicer, this makes the entire process of data analysis transparent, insofar as every step from raw reads to published figure is publicly available as open source code.

Keywords: 3D genomics; Hi-C; contact domains; contact map; enhancers; genome architecture; loop extrusion; loops; nuclear architecture; visualization.

MeSH terms

Cloud Computing
Computational Biology / methods*
Computer Graphics
Computers
Data Analysis
Genome / genetics
Image Processing, Computer-Assisted / methods*
Internet
Reproducibility of Results
Software

Abstract

MeSH terms

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