TY - JOUR
T1 - Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud
AU - Wang, Liya
AU - Lu, Zhenyuan
AU - delaBastide, Melissa
AU - Van Buren, Peter
AU - Wang, Xiaofei
AU - Ghiban, Cornel
AU - Regulski, Michael
AU - Drenkow, Jorg
AU - Xu, Xiaosa
AU - Ortiz-Ramirez, Carlos
AU - Marco, Cristina F.
AU - Goodwin, Sara
AU - Dobin, Alexander
AU - Birnbaum, Kenneth D.
AU - Jackson, David P.
AU - Martienssen, Robert A.
AU - McCombie, William R.
AU - Micklos, David A.
AU - Schatz, Michael C.
AU - Ware, Doreen H.
AU - Gingeras, Thomas R.
N1 - Publisher Copyright:
© Copyright © 2020 Wang, Lu, delaBastide, Van Buren, Wang, Ghiban, Regulski, Drenkow, Xu, Ortiz-Ramirez, Marco, Goodwin, Dobin, Birnbaum, Jackson, Martienssen, McCombie, Micklos, Schatz, Ware and Gingeras.
PY - 2020/3/31
Y1 - 2020/3/31
N2 - 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 enhanced 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 MaizeCODE data management. These include publicly accessible scientific workflows for the 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 the 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.
AB - 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 enhanced 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 MaizeCODE data management. These include publicly accessible scientific workflows for the 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 the 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.
KW - ENCODE
KW - bioinformatics
KW - cloud computing
KW - functional annotations
KW - workflows
UR - http://www.scopus.com/inward/record.url?scp=85083316749&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=85083316749&partnerID=8YFLogxK
U2 - 10.3389/fpls.2020.00289
DO - 10.3389/fpls.2020.00289
M3 - Article
AN - SCOPUS:85083316749
SN - 1664-462X
VL - 11
JO - Frontiers in Plant Science
JF - Frontiers in Plant Science
M1 - 289
ER -