Abstract 5331: GenomeSpace: An environment for frictionless bioinformatics

• Published in: Cancer research (Chicago, Ill.) Ill.), 2014-10, Vol.74 (19_Supplement), p.5331-5331
• Main Authors: Reich, Michael M., Liefeld, John, Ocana, Marco, Jang, Donkeung, Robinson, James, Carr, Peter, Hill, Barbara, Tabor, Thorin, Thorvaldsdottir, Helga, Regev, Aviv, Mesirov, Jill P.
• Format: Article
• Language: English
• ISSN: 0008-5472; 1538-7445
• DOI: 10.1158/1538-7445.AM2014-5331

Over the past several years, cancer genome characterization initiatives such as The Cancer Genome Atlas and the International Cancer Genome Consortium have produced an explosion of genomic data. These efforts, together with the proliferation of repositories for small-molecule screens and large-scale data production efforts to discover the breadth of genomic variation in humans, offer a new era of potential for the understanding of the basic mechanisms of cancer and identification of novel treatments. Comprehensive analysis of these datasets requires the coordinated use of Web-based applications and data repositories, desktop analysis tools and visualizers, and single-purpose algorithms. However, the effort required to transfer data between tools, convert between data formats, and manage results often prevents researchers from utilizing the wealth of methods available to them. Many integrative genomics and translational “bench to bedside” discoveries are possible with combinations of existing tools, but the necessary transitions between them puts them out of the reach of most researchers. GenomeSpace, http://www.genomespace.org, is an environment that brings together diverse computational tools, enabling scientists without programming skills to easily combine their capabilities. It aims to offer a common space to create, manipulate and share an ever-growing range of genomic analysis tools. GenomeSpace features support for cloud-based data storage and analysis, multi-tool analytic workflows, automatic conversion of data formats, and ease of connecting new tools to the environment. A set of six “GenomeSpace-enabled” seed tools developed by collaborating organizations provides a comprehensive platform for the analysis of cancer data: Cytoscape (UCSD), Galaxy (Penn State University), GenePattern (Broad Institute), Genomica (Weitzmann Institute), Integrative Genomics Viewer (Broad Institute), and the UCSC Genome Browser (UCSC). Its open architecture has driven its adoption by a number of additional tools, including ArrayExpress, Cistrome, the Cancer Cell Line Encyclopedia, Project Achilles Portal, and Multiple Myeloma Genomics Portal, with new tools and resources being released regularly. We show how researchers can use GenomeSpace to effortlessly combine the capabilities of all of these tools in several cancer research scenarios. Citation Format: Michael M. Reich, John Liefeld, Marco Ocana, Donkeung Jang, James Robinson, Peter Carr, Barbara Hill, Thorin Tabor,