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

35 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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10.1038/nmeth.3732

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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

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title = "Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace",

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.",

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

note = "Funding Information: 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). Publisher Copyright: {\textcopyright} 2016 Nature America, Inc.",

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doi = "10.1038/nmeth.3732",

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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

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AU - Qu, Kun

AU - Garamszegi, Sara

AU - Wu, Felix

AU - Thorvaldsdottir, Helga

AU - Liefeld, Ted

AU - Ocana, Marco

AU - Borges-Rivera, Diego

AU - Pochet, Nathalie

AU - Robinson, James T.

AU - Demchak, Barry

AU - Hull, Tim

AU - Ben-Artzi, Gil

AU - Blankenberg, Daniel

AU - Barber, Galt P.

AU - Lee, Brian T.

AU - Kuhn, Robert M.

AU - Nekrutenko, Anton

AU - Segal, Eran

AU - Ideker, Trey

AU - Reich, Michael

AU - Regev, Aviv

AU - Y Chang, Howard

AU - Mesirov, Jill P.

N1 - Funding Information: 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). Publisher Copyright: © 2016 Nature America, Inc.

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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

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