The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research

Sheila M. Reynolds; Michael Miller; Phyliss Lee; Kalle Leinonen; Suzanne M. Paquette; Zack Rodebaugh; Abigail Hahn; David L. Gibbs; Joseph Slagel; William J. Longabaugh; Varsha Dhankani; Madelyn Reyes; Todd Pihl; Mark Backus; Matthew Bookman; Nicole Deflaux; Jonathan Bingham; David Pot; Ilya Shmulevich

doi:10.1158/0008-5472.CAN-17-0617

The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research

Sheila M. Reynolds
, Michael Miller
, Phyliss Lee
, Kalle Leinonen
, Suzanne M. Paquette
, Zack Rodebaugh
, Abigail Hahn
, David L. Gibbs
, Joseph Slagel
, William J. Longabaugh
, Varsha Dhankani
, Madelyn Reyes
, Todd Pihl
, Mark Backus
, Matthew Bookman
, Nicole Deflaux
, Jonathan Bingham
, David Pot
, Ilya Shmulevich

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

50 Scopus citations

Abstract

The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.org. Cancer Res; 77(21); e7-10.

Original language	English
Pages (from-to)	e7-e10
Journal	Cancer Research
Volume	77
Issue number	21
DOIs	https://doi.org/10.1158/0008-5472.CAN-17-0617
State	Published - Nov 1 2017

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10.1158/0008-5472.CAN-17-0617

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Reynolds, S. M., Miller, M., Lee, P., Leinonen, K., Paquette, S. M., Rodebaugh, Z., Hahn, A., Gibbs, D. L., Slagel, J., Longabaugh, W. J., Dhankani, V., Reyes, M., Pihl, T., Backus, M., Bookman, M., Deflaux, N., Bingham, J., Pot, D., & Shmulevich, I. (2017). The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research. Cancer Research, 77(21), e7-e10. https://doi.org/10.1158/0008-5472.CAN-17-0617

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title = "The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research",

abstract = "The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.org. Cancer Res; 77(21); e7-10.",

author = "Reynolds, \{Sheila M.\} and Michael Miller and Phyliss Lee and Kalle Leinonen and Paquette, \{Suzanne M.\} and Zack Rodebaugh and Abigail Hahn and Gibbs, \{David L.\} and Joseph Slagel and Longabaugh, \{William J.\} and Varsha Dhankani and Madelyn Reyes and Todd Pihl and Mark Backus and Matthew Bookman and Nicole Deflaux and Jonathan Bingham and David Pot and Ilya Shmulevich",

note = "Publisher Copyright: {\textcopyright} 2017 American Association for Cancer Research.",

year = "2017",

month = nov,

day = "1",

doi = "10.1158/0008-5472.CAN-17-0617",

language = "English",

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Reynolds, SM, Miller, M, Lee, P, Leinonen, K, Paquette, SM, Rodebaugh, Z, Hahn, A, Gibbs, DL, Slagel, J, Longabaugh, WJ, Dhankani, V, Reyes, M, Pihl, T, Backus, M, Bookman, M, Deflaux, N, Bingham, J, Pot, D & Shmulevich, I 2017, 'The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research', Cancer Research, vol. 77, no. 21, pp. e7-e10. https://doi.org/10.1158/0008-5472.CAN-17-0617

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AU - Leinonen, Kalle

AU - Paquette, Suzanne M.

AU - Rodebaugh, Zack

AU - Hahn, Abigail

AU - Gibbs, David L.

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AU - Longabaugh, William J.

AU - Dhankani, Varsha

AU - Reyes, Madelyn

AU - Pihl, Todd

AU - Backus, Mark

AU - Bookman, Matthew

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AU - Shmulevich, Ilya

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The ISB cancer genomics cloud: A flexible cloud-based platform for cancer genomics research

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