SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data

Liya Wang; Zhenyuan Lu; Peter Van Buren; Doreen Ware

doi:10.1007/978-1-0716-2067-0_10

SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data

Methods Mol Biol. 2022:2443:197-209. doi: 10.1007/978-1-0716-2067-0_10.

Authors

Liya Wang¹, Zhenyuan Lu¹, Peter Van Buren¹, Doreen Ware^{2

3}

Affiliations

¹ Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA.
² Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA. ware@cshl.edu.
³ USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY, USA. ware@cshl.edu.

PMID: 35037207
DOI: 10.1007/978-1-0716-2067-0_10

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 one 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.

Keywords: BSA; Distributed cloud computing; Genetic variation; Plant ENCODE; Plant genomics; Visualization; Workflow management system.

Publication types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH terms

Computational Biology
Genome, Plant
Genomics* / methods
Information Storage and Retrieval
Software*
Workflow