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ARS Home » Northeast Area » Ithaca, New York » Robert W. Holley Center for Agriculture & Health » Plant, Soil and Nutrition Research » Research » Publications at this Location » Publication #383732

Research Project: Mapping Crop Genome Functions for Biology-Enabled Germplasm Improvement

Location: Plant, Soil and Nutrition Research

Title: SciApps: an automated platform for processing and distribution of plant genomics data

item WANG, LIYA - Cold Spring Harbor Laboratory
item LU, ZHENYUAN - Cold Spring Harbor Laboratory
item BUREN, PETER VAN - Cold Spring Harbor Laboratory
item Ware, Doreen

Submitted to: Book Chapter
Publication Type: Book / Chapter
Publication Acceptance Date: 10/19/2020
Publication Date: N/A
Citation: N/A

Interpretive Summary:

Technical Abstract: SciApps is an open-source, web-based platform for processing, storing, visualizing, and distributing genomic data and analysis results. Built upon the Tapis (formerly Agave) platform, SciApps brings users TB-scale of data storage via CyVerse Data Store and over 1 million CPUs via the eXtreme Science and Engineering Discovery Environment (XSEDE) resources at Texas Advanced Computing Center (TACC). SciApps provides users ways to chain individual jobs into automated and reproducible workflows in a distributed cloud and provides a management system for data, associated metadata, individual analysis jobs, and multi-step workflows. This chapter provides examples of how to (1) submitting, managing, constructing workflows, (2) using public workflows for Bulked Segregant Analysis (BSA), (3) constructing a Data Analysis Center (DAC) and Data Coordination Center (DCC) for the plant ENCODE project.