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SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data

View ORCID ProfileLiya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz Ramirez, Cristina F. Marco, Jason Williams, Alexander Dobin, Kenneth D. Birnbaum, David P. Jackson, Robert A. Martienssen, William R. McCombie, David A. Micklos, Michael C. Schatz, Doreen H. Ware, Thomas R. Gingeras
doi: https://doi.org/10.1101/852269
Liya Wang
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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  • For correspondence: wangli@cshl.edu
Zhenyuan Lu
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Melissa delaBastide
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Peter Van Buren
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Xiaofei Wang
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Cornel Ghiban
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Michael Regulski
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Jorg Drenkow
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Xiaosa Xu
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Carlos Ortiz Ramirez
2New York University, New York, NY
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Cristina F. Marco
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Jason Williams
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Alexander Dobin
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Kenneth D. Birnbaum
2New York University, New York, NY
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David P. Jackson
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Robert A. Martienssen
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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William R. McCombie
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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David A. Micklos
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Michael C. Schatz
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
3Johns Hopkins University, Baltimore, MD
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Doreen H. Ware
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
4USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, United States
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Thomas R. Gingeras
1Cold Spring Harbor Laboratory, Cold Spring Harbor, NY
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Abstract

MaizeCODE is a project aimed at identifying and analyzing functional elements in the maize genome. In its initial phase, MaizeCODE assayed up to five tissues from four maize strains (B73, NC350, W22, TIL11) by RNA-Seq, Chip-Seq, RAMPAGE, and small RNA sequencing. To facilitate reproducible science and provide both human and machine access to the MaizeCODE data, we developed SciApps, a cloud-based portal, for analysis and distribution of both raw data and analysis results. Based on the SciApps workflow platform, we generated new components to support the complete cycle of the MaizeCODE data management. These include publicly accessible scientific workflows for reproducible and shareable analysis of various functional data, a RESTful API for batch processing and distribution of data and metadata, a searchable data page that lists each MaizeCODE experiment as a reproducible workflow, and integrated JBrowse genome browser tracks linked with workflows and metadata. The SciApps portal is a flexible platform that allows integration of new analysis tools, workflows, and genomic data from multiple projects. Through metadata and a ready-to-compute cloud-based platform, the portal experience improves access to the MaizeCODE data and facilitates its analysis.

Footnotes

  • https://www.sciapps.org

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
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Posted November 23, 2019.
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SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data
Liya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz Ramirez, Cristina F. Marco, Jason Williams, Alexander Dobin, Kenneth D. Birnbaum, David P. Jackson, Robert A. Martienssen, William R. McCombie, David A. Micklos, Michael C. Schatz, Doreen H. Ware, Thomas R. Gingeras
bioRxiv 852269; doi: https://doi.org/10.1101/852269
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SciApps: A Cloud-Based Platform for Analyses and Distribution of the MaizeCODE data
Liya Wang, Zhenyuan Lu, Melissa delaBastide, Peter Van Buren, Xiaofei Wang, Cornel Ghiban, Michael Regulski, Jorg Drenkow, Xiaosa Xu, Carlos Ortiz Ramirez, Cristina F. Marco, Jason Williams, Alexander Dobin, Kenneth D. Birnbaum, David P. Jackson, Robert A. Martienssen, William R. McCombie, David A. Micklos, Michael C. Schatz, Doreen H. Ware, Thomas R. Gingeras
bioRxiv 852269; doi: https://doi.org/10.1101/852269

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