Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu; Sara Garamszegi; Felix Wu; Helga Thorvaldsdottir; Ted Liefeld; Marco Ocana; Diego Borges-Rivera; Nathalie Pochet; James T. Robinson; Barry Demchak; Tim Hull; Gil Ben-Artzi; Daniel Blankenberg; Galt P. Barber; Brian T. Lee; Robert M. Kuhn; Anton Nekrutenko; Eran Segal; Trey Ideker; Michael Reich; Aviv Regev; Howard Y Chang; Jill P. Mesirov

doi:10.1038/nmeth.3732

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

Kun Qu, Sara Garamszegi, Felix Wu, Helga Thorvaldsdottir, Ted Liefeld, Marco Ocana, Diego Borges-Rivera, Nathalie Pochet, James T. Robinson, Barry Demchak, Tim Hull, Gil Ben-Artzi, Daniel Blankenberg, Galt P. Barber, Brian T. Lee, Robert M. Kuhn, Anton Nekrutenko, Eran Segal, Trey Ideker, Michael ReichAviv Regev, Howard Y Chang, Jill P. Mesirov

Research output: Contribution to journal › Article › peer-review

26 Scopus citations

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.

Original language	English (US)
Pages (from-to)	245-247
Number of pages	3
Journal	Nature methods
Volume	13
Issue number	3
DOIs	https://doi.org/10.1038/nmeth.3732
State	Published - Feb 25 2016

All Science Journal Classification (ASJC) codes

Biotechnology
Biochemistry
Molecular Biology
Cell Biology

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Qu, K., Garamszegi, S., Wu, F., Thorvaldsdottir, H., Liefeld, T., Ocana, M., Borges-Rivera, D., Pochet, N., Robinson, J. T., Demchak, B., Hull, T., Ben-Artzi, G., Blankenberg, D., Barber, G. P., Lee, B. T., Kuhn, R. M., Nekrutenko, A., Segal, E., Ideker, T., ... Mesirov, J. P. (2016). Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. Nature methods, 13(3), 245-247. https://doi.org/10.1038/nmeth.3732

Qu, Kun ; Garamszegi, Sara ; Wu, Felix ; Thorvaldsdottir, Helga ; Liefeld, Ted ; Ocana, Marco ; Borges-Rivera, Diego ; Pochet, Nathalie ; Robinson, James T. ; Demchak, Barry ; Hull, Tim ; Ben-Artzi, Gil ; Blankenberg, Daniel ; Barber, Galt P. ; Lee, Brian T. ; Kuhn, Robert M. ; Nekrutenko, Anton ; Segal, Eran ; Ideker, Trey ; Reich, Michael ; Regev, Aviv ; Y Chang, Howard ; Mesirov, Jill P. / Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. In: Nature methods. 2016 ; Vol. 13, No. 3. pp. 245-247.

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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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Qu, K, Garamszegi, S, Wu, F, Thorvaldsdottir, H, Liefeld, T, Ocana, M, Borges-Rivera, D, Pochet, N, Robinson, JT, Demchak, B, Hull, T, Ben-Artzi, G, Blankenberg, D, Barber, GP, Lee, BT, Kuhn, RM, Nekrutenko, A, Segal, E, Ideker, T, Reich, M, Regev, A, Y Chang, H & Mesirov, JP 2016, 'Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace', Nature methods, vol. 13, no. 3, pp. 245-247. https://doi.org/10.1038/nmeth.3732

Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace. / Qu, Kun; Garamszegi, Sara; Wu, Felix; Thorvaldsdottir, Helga; Liefeld, Ted; Ocana, Marco; Borges-Rivera, Diego; Pochet, Nathalie; Robinson, James T.; Demchak, Barry; Hull, Tim; Ben-Artzi, Gil; Blankenberg, Daniel; Barber, Galt P.; Lee, Brian T.; Kuhn, Robert M.; Nekrutenko, Anton; Segal, Eran; Ideker, Trey; Reich, Michael; Regev, Aviv; Y Chang, Howard; Mesirov, Jill P.

In: Nature methods, Vol. 13, No. 3, 25.02.2016, p. 245-247.

Research output: Contribution to journal › Article › peer-review

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AU - Garamszegi, Sara

AU - Wu, Felix

AU - Thorvaldsdottir, Helga

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AU - Ocana, Marco

AU - Borges-Rivera, Diego

AU - Pochet, Nathalie

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AU - Demchak, Barry

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AU - Ben-Artzi, Gil

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AU - Barber, Galt P.

AU - Lee, Brian T.

AU - Kuhn, Robert M.

AU - Nekrutenko, Anton

AU - Segal, Eran

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AU - Reich, Michael

AU - Regev, Aviv

AU - Y Chang, Howard

AU - Mesirov, Jill P.

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