Cloud-based introduction to BASH programming for biologists

Abstract

Abstract This manuscript describes the development of a resource module that is part of a learning platform named ‘NIGMS Sandbox for Cloud-based Learning’, https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial authored by National Institute of General Medical Sciences: NIGMS Sandbox: A Learning Platform toward Democratizing Cloud Computing for Biomedical Research at the beginning of this supplement. This module delivers learning materials introducing the utility of the BASH (Bourne Again Shell) programming language for genomic data analysis in an interactive format that uses appropriate cloud resources for data access and analyses. The next-generation sequencing revolution has generated massive amounts of novel biological data from a multitude of platforms that survey an ever-growing list of genomic modalities. These data require significant downstream computational and statistical analyses to glean meaningful biological insights. However, the skill sets required to generate these data are vastly different from the skills required to analyze these data. Bench scientists that generate next-generation data often lack the training required to perform analysis of these datasets and require support from bioinformatics specialists. Dedicated computational training is required to empower biologists in the area of genomic data analysis, however, learning to efficiently leverage a command line interface is a significant barrier in learning how to leverage common analytical tools. Cloud platforms have the potential to democratize access to the technical tools and computational resources necessary to work with modern sequencing data, providing an effective framework for bioinformatics education. This module aims to provide an interactive platform that slowly builds technical skills and knowledge needed to interact with genomics data on the command line in the Cloud. The sandbox format of this module enables users to move through the material at their own pace and test their grasp of the material with knowledge self-checks before building on that material in the next sub-module. This manuscript describes the development of a resource module that is part of a learning platform named ``NIGMS Sandbox for Cloud-based Learning'' https://github.com/NIGMS/NIGMS-Sandbox. The overall genesis of the Sandbox is described in the editorial NIGMS Sandbox [1] at the beginning of this Supplement. This module delivers learning materials on the analysis of bulk and single-cell ATAC-seq data in an interactive format that uses appropriate cloud resources for data access and analyses.