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      WashU Epigenome Browser update 2019

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          Abstract

          The WashU Epigenome Browser ( https://epigenomegateway.wustl.edu/) provides visualization, integration and analysis tools for epigenomic datasets. Since 2010, it has provided the scientific community with data from large consortia including the Roadmap Epigenomics and the ENCODE projects. Recently, we refactored the codebase, redesigned the user interface, and developed various novel features. New features include: (i) visualization using virtual reality (VR), which has implications in biology education and the study of 3D chromatin structure; (ii) expanded public data hubs, including data from the 4DN, ENCODE, Roadmap Epigenomics, TaRGET, IHEC and TCGA consortia; (iii) a more responsive user interface; (iv) a history of interactions, which enables undo and redo; (v) a feature we call Live Browsing, which allows multiple users to collaborate remotely on the same session; (vi) the ability to visualize local tracks and data hubs. Amazon Web Services also hosts the redesign at  https://epigenomegateway.org/.

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          HiGlass: web-based visual exploration and analysis of genome interaction maps

          Peter Kerpedjiev, Nezar Abdennur, Fritz Lekschas … (2018)
          We present HiGlass, an open source visualization tool built on web technologies that provides a rich interface for rapid, multiplex, and multiscale navigation of 2D genomic maps alongside 1D genomic tracks, allowing users to combine various data types, synchronize multiple visualization modalities, and share fully customizable views with others. We demonstrate its utility in exploring different experimental conditions, comparing the results of analyses, and creating interactive snapshots to share with collaborators and the broader public. HiGlass is accessible online at http://higlass.io and is also available as a containerized application that can be run on any platform. Electronic supplementary material The online version of this article (10.1186/s13059-018-1486-1) contains supplementary material, which is available to authorized users.
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            The Cancer Genome Atlas: Creating Lasting Value beyond Its Data.

            Carolyn Hutter, Jean Claude Zenklusen (2018)
            The Cancer Genome Atlas (TCGA) team now presents the Pan-Cancer Atlas, investigating different aspects of cancer biology by analyzing the data generated during the 10+ years of the TCGA project.
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              Juicebox.js Provides a Cloud-Based Visualization System for Hi-C Data

              James Robinson, Douglass Turner, Neva Durand … (2018)
              SUMMARY 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.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Nucleic Acids Res
                Journal ID (iso-abbrev): Nucleic Acids Res
                Journal ID (publisher-id): nar
                Title: Nucleic Acids Research
                Publisher: Oxford University Press
                ISSN (Print): 0305-1048
                ISSN (Electronic): 1362-4962
                Publication date (Print): 02 July 2019
                Publication date (Electronic): 05 June 2019
                Publication date PMC-release: 05 June 2019
                Volume: 47
                Issue: W1
                Pages: W158-W165
                Affiliations
                [1 ]Department of Genetics, Washington University School of Medicine, St. Louis, MO, USA
                [2 ]The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO, USA
                Author notes
                To whom correspondence should be addressed. Tel: +1 314 286 0865; Email: twang@ 123456wustl.edu

                The first two authors contributed equally to this work.

                Article
                Publisher ID: gkz348
                DOI: 10.1093/nar/gkz348
                PMC ID: 6602459
                PubMed ID: 31165883
                SO-VID: e4fe709d-b0cd-4122-9ad3-c6959bbc0c33
                Copyright © © The Author(s) 2019. Published by Oxford University Press on behalf of Nucleic Acids Research.
                License:

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@ 123456oup.com

                History
                Date accepted : 31 May 2019
                Date revision received : 23 April 2019
                Date received : 08 February 2019
                Page count
                Pages: 8
                Funding
                Funded by: NIH 10.13039/100000002
                Award ID: R01HG007354
                Award ID: R01HG007175
                Award ID: R01ES024992
                Award ID: U01CA200060
                Award ID: U24ES026699
                Award ID: U01HG009391
                Funded by: American Cancer Society 10.13039/100000048
                Award ID: RSG-14-049-01-DMC
                Categories
                Subject: Web Server Issue

                ScienceOpen disciplines: Genetics
                Data availability:
                ScienceOpen disciplines: Genetics

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