What Is GenomeSpace?
GenomeSpace is a cloud-based interoperability framework to support integrative genomics analysis through an easy-to-use Web interface. GenomeSpace provides access to a diverse range of bioinformatics tools, and bridges the gaps between the tools, making it easy to leverage the available analyses and visualizations in each of them. The tools retain their native look and feel, with GenomeSpace providing frictionless conduits between them through a lightweight interoperability layer. GenomeSpace does not perform any analyses itself; these are done within the member tools wherever they live – desktop, Web service, cloud, in-house server, etc. Rather, GenomeSpace provides tool selection and launch capabilities, and acts as a data highway automatically reformatting data as required when results move from the output of one tool to input for the next.
GenomeSpace started as a partnership between the Mesirov and Regev laboratories at the Broad Institute, the Chang laboratory at Stanford University, the Ideker laboratory at the University of California, San Diego, the Nekrutenko laboratory at Pennsylvania State University, the Segal laboratory at the Weizmann Institute of Science, and the Haussler and Kent laboratories at the University of California, Santa Cruz. This collaboration between leading researchers in the field and developers of some of the most prominent and widely-used tools for genomics analysis, sought to seed GenomeSpace with strong capabilities, drive its development with ongoing genomic research projects, and build an open environment for other tools and packages.
On April 25 of 2012, we released an open source, proof-of-principle beta version of GenomeSpace and announced its availability at the Bio-IT World conference. The initial tools were: Cytoscape, Galaxy, GenePattern, Genomica, Integrative Genomics Viewer (IGV), and the UCSC Genome Table Browser. GenomeSpace’s lightweight cooperative approach de-emphasizes strong typing and formal descriptive models, and quickly yielded a workable, agile framework that allows participating tools to retain their own identity while seamlessly interoperating with others. Since the initial beta release, a number of other tools and data sources have been added. A complete and current list is on the Tools page.
A quick overview of how GenomeSpace can facilitate your science.
A quick overview of the tools and applications available through GenomeSpace.
Short guides that provide outlines for performing specific common tasks. These can help you get your hands on the GenomeSpace functionality.