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

Department of Computer Science and Applied Mathematics

Weizmann Institute of Science

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

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
Pages (from-to)	245-247
Number of pages	3
Journal	Nature Methods
Volume	13
Issue number	3
Early online date	18 Jan 2016
DOIs	https://doi.org/10.1038/nmeth.3732
State	Published - 25 Feb 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

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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.\}",

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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

TY - JOUR

T1 - Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

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.

PY - 2016/2/25

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AB - 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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DO - 10.1038/nmeth.3732

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SP - 245

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Integrative genomic analysis by interoperation of bioinformatics tools in GenomeSpace

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