Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud

Wang, L., Lu, Z., Delabastide, M., Van Buren, P., Wang, X., Ghiban, C., Regulski, M., Drenkow, J., Xu, X., Ortiz-Ramirez, C., Marco, C.F., Goodwin, S., Dobin, A., Birnbaum, K. D., Jackson, D. P., Martienssen, R. A., McCombie, W. R., Micklos, D. A., Schatz, M. C., Ware, D. H., Gingeras, T. R. (March 2020) Management, Analyses, and Distribution of the MaizeCODE Data on the Cloud. Frontiers in Plant Science, 11 (289). ISSN 1664-462X (Public Dataset)

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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 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.

Item Type: Paper
Subjects: bioinformatics
bioinformatics > genomics and proteomics > genetics & nucleic acid processing
bioinformatics > genomics and proteomics
organism description > plant > maize
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > genomes
organism description > plant
CSHL Authors:
Communities: CSHL labs > Gingeras lab
CSHL labs > Jackson lab
CSHL labs > Martienssen lab
CSHL labs > McCombie lab
CSHL labs > Schatz lab
CSHL labs > Ware lab
CSHL labs > Dobin Lab
Depositing User: Adrian Gomez
Date: 31 March 2020
Date Deposited: 17 Apr 2020 15:11
Last Modified: 01 Feb 2024 19:17
PMCID: PMC7136414
Related URLs:
Dataset ID:
  • https://www.ncbi.nlm.nih.gov/bioproject/380952
URI: https://repository.cshl.edu/id/eprint/39242

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