Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu^#¹, Sara Garamszegi^#², Felix Wu^#², Helga Thorvaldsdottir², Ted Liefeld^{2

3}, Marco Ocana^{2

3}, Diego Borges-Rivera⁴, Nathalie Pochet^{2

5}, James T Robinson^{2

3}, Barry Demchak³, Tim Hull³, Gil Ben-Artzi^{6

7}, Daniel Blankenberg⁸, Galt P Barber⁹, Brian T Lee⁹, Robert M Kuhn⁹, Anton Nekrutenko⁸, Eran Segal⁶, Trey Ideker³, Michael Reich^{2

3}, Aviv Regev^{2

4

10}, Howard Y Chang^{1

11}, Jill P Mesirov^{2

3}

Affiliations

¹ Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
² The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Medicine, University of California, San Diego, La Jolla, USA.
⁴ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
⁷ Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
⁸ Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.
⁹ UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
¹⁰ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹¹ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.

^# Contributed equally.

PMID: 26780094
PMCID: PMC4767623
DOI: 10.1038/nmeth.3732

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu et al. Nat Methods. 2016 Mar.

. 2016 Mar;13(3):245-247.

doi: 10.1038/nmeth.3732. Epub 2016 Jan 18.

Authors

Affiliations

¹ Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA, USA.
² The Broad Institute of MIT and Harvard, Cambridge, MA, USA.
³ Department of Medicine, University of California, San Diego, La Jolla, USA.
⁴ Department of Biology, Massachusetts Institute of Technology, Cambridge, MA, USA.
⁵ Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.
⁶ Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.
⁷ Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.
⁸ Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, USA.
⁹ UC Santa Cruz Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
¹⁰ Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, MA, USA.
¹¹ Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA.

^# Contributed equally.

PMID: 26780094
PMCID: PMC4767623
DOI: 10.1038/nmeth.3732

Abstract

Complex biomedical analyses require the use of multiple software tools in concert and remain challenging for much of the biomedical research community. We introduce GenomeSpace (http://www.genomespace.org), a cloud-based, cooperative community resource that currently supports the streamlined interaction of 20 bioinformatics tools and data resources. To facilitate integrative analysis by non-programmers, it offers a growing set of 'recipes', short workflows to guide investigators through high-utility analysis tasks.

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Figures

**Figure 1. The GenomeSpace environment for interoperation of bioinformatics tools**

See this image and copyright information in PMC

References

1. Lander ES, et al. Nature. 2001;409:860. - PubMed
1. Demchak B, et al. F1000Research. 2014;3:151. - PMC - PubMed
1. Shannon P, et al. Genome Res. 2003;13:2498. - PMC - PubMed
1. Giardine B, et al. Genome Res. 2005;15:1451. - PMC - PubMed
1. Reich M, et al. Nat Genet. 2006;38:500. - PubMed

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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Affiliations

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Authors

Affiliations

Abstract

Figures

References

Publication types

MeSH terms

Grants and funding

LinkOut - more resources

Full Text Sources

Other Literature Sources