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.

Access optionsAccess options

Rent or Buy article

Get time limited or full article access on ReadCube.

from$8.99

All prices are NET prices.

References

  1. 1.

    et al. F1000Res. 3, 151 (2014).

  2. 2.

    et al. Genome Res. 13, 2498–2504 (2003).

  3. 3.

    et al. Genome Res. 15, 1451–1455 (2005).

  4. 4.

    et al. Nat. Genet. 38, 500–501 (2006).

  5. 5.

    , , & Nat. Genet. 36, 1090–1098 (2004).

  6. 6.

    et al. Nat. Biotechnol. 29, 24–26 (2011).

  7. 7.

    et al. Nucleic Acids Res. 32, D493–D496 (2004).

  8. 8.

    et al. Nat. Genet. 40, 499–507 (2008).

  9. 9.

    et al. Cell Stem Cell 2, 333–344 (2008).

  10. 10.

    , & Molecular Cloning: A Laboratory Manual vol. 3 (Cold Spring Harbor Laboratory Press, 1989).

  11. 11.

    et al. Nature 442, 818–822 (2006).

  12. 12.

    & Oncogene 24, 5676–5692 (2005).

  13. 13.

    , , , & Bioinformatics 26, 1779–1780 (2010).

  14. 14.

    et al. Biotechniques 34, 374–378 (2003).

  15. 15.

    , , & in Software Architecture, 2008. WICSA 2008. Seventh Working IEEE/IFIP Conference (eds. Kruchten, P., Garlan, D. & Woods, E.) 95–104 (IEEE Computer Society, 2008).

  16. 16.

    , , & BMC Bioinformatics 7, 176 (2006).

Download references

Acknowledgements

We thank other members of the GenomeSpace and GenePattern Teams for their contributions and input: P. Carr, B. Hill-Meyers, S.H. Lee and T. Tabor (Broad Institute of MIT and Harvard); J. Zhang (Stanford University); and H. Carter and M. Smoot (University of California, San Diego). Special thanks to D. Haussler and J. Kent (University of California, Santa Cruz) for their involvement in the nascent stages of the GenomeSpace project. We thank J. Bistline for help with the citations and figures, and L. Gaffney for help with the figures. This work has been supported by US National Institutes of Health–National Human Genome Research Institute P01 HG005062 and U41 HG007517, with additional initial support from Amazon Web Services (AWS).

Author information

Author notes

    • Kun Qu
    • , Sara Garamszegi
    •  & Felix Wu

    These authors contributed equally to this work.

Affiliations

  1. Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA.

    • Kun Qu
    •  & Howard Y Chang
  2. The Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA.

    • Sara Garamszegi
    • , Felix Wu
    • , Helga Thorvaldsdottir
    • , Ted Liefeld
    • , Marco Ocana
    • , Nathalie Pochet
    • , James T Robinson
    • , Michael Reich
    • , Aviv Regev
    •  & Jill P Mesirov
  3. Department of Medicine, University of California, San Diego, La Jolla, California, USA.

    • Ted Liefeld
    • , Marco Ocana
    • , James T Robinson
    • , Barry Demchak
    • , Tim Hull
    • , Trey Ideker
    • , Michael Reich
    •  & Jill P Mesirov
  4. Department of Biology, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Diego Borges-Rivera
    •  & Aviv Regev
  5. Program in Translational NeuroPsychiatric Genomics, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, USA.

    • Nathalie Pochet
  6. Department of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot, Israel.

    • Gil Ben-Artzi
    •  & Eran Segal
  7. Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot, Israel.

    • Gil Ben-Artzi
  8. Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA.

    • Daniel Blankenberg
    •  & Anton Nekrutenko
  9. UC Santa Cruz Genomics Institute, University of California, Santa Cruz, Santa Cruz, California, USA.

    • Galt P Barber
    • , Brian T Lee
    •  & Robert M Kuhn
  10. Howard Hughes Medical Institute, Massachusetts Institute of Technology, Cambridge, Massachusetts, USA.

    • Aviv Regev
  11. Howard Hughes Medical Institute, Stanford University, Stanford, California, USA.

    • Howard Y Chang

Authors

  1. Search for Kun Qu in:

  2. Search for Sara Garamszegi in:

  3. Search for Felix Wu in:

  4. Search for Helga Thorvaldsdottir in:

  5. Search for Ted Liefeld in:

  6. Search for Marco Ocana in:

  7. Search for Diego Borges-Rivera in:

  8. Search for Nathalie Pochet in:

  9. Search for James T Robinson in:

  10. Search for Barry Demchak in:

  11. Search for Tim Hull in:

  12. Search for Gil Ben-Artzi in:

  13. Search for Daniel Blankenberg in:

  14. Search for Galt P Barber in:

  15. Search for Brian T Lee in:

  16. Search for Robert M Kuhn in:

  17. Search for Anton Nekrutenko in:

  18. Search for Eran Segal in:

  19. Search for Trey Ideker in:

  20. Search for Michael Reich in:

  21. Search for Aviv Regev in:

  22. Search for Howard Y Chang in:

  23. Search for Jill P Mesirov in:

Contributions

M.R., A.R. and J.P.M. conceived of the GenomeSpace concept. T.L., M.O. and M.R. designed and implemented the GenomeSpace software. K.Q., S.G., F.W. and N.P. implemented the driving biological projects within GenomeSpace with supervision and input from A.R., H.Y.C. and J.P.M. The recipes were implemented by S.G., F.W. and D.B.-R. The GenomeSpace seed tools were added to the system by J.T.R., B.D., T.H., G.B.-A., D.B., G.P.B., B.T.L., R.M.K., A.N., E.S. and T.I., who also consulted on the GenomeSpace architecture. H.T., M.R., A.R., H.Y.C. and J.P.M. supervised the GenomeSpace project. K.Q., S.G., F.W., H.T., M.R., H.C., A.R. and J.P.M. wrote the manuscript. All authors reviewed and approved the final manuscript as submitted.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Jill P Mesirov.

Integrated supplementary information

Supplementary information

PDF files

  1. 1.

    Supplementary Text and Figures

    Supplementary Figures 1–11, Supplementary Table 1 and Supplementary Notes 1–3.

About this article

Publication history

Received

Accepted

Published

DOI

https://doi.org/10.1038/nmeth.3732

Further reading