PDF(Pubmed)
Abstract：
This study 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 at the beginning of this Supplement. This module delivers learning materials on de novo transcriptome assembly using Nextflow in an interactive format that uses appropriate cloud resources for data access and analysis. Cloud computing is a powerful new means by which biomedical researchers can access resources and capacity that were previously either unattainable or prohibitively expensive. To take advantage of these resources, however, the biomedical research community needs new skills and knowledge. We present here a cloud-based training module, developed in conjunction with Google Cloud, Deloitte Consulting, and the NIH STRIDES Program, that uses the biological problem of de novo transcriptome assembly to demonstrate and teach the concepts of computational workflows (using Nextflow) and cost- and resource-efficient use of Cloud services (using Google Cloud Platform). Our work highlights the reduced necessity of on-site computing resources and the accessibility of cloud-based infrastructure for bioinformatics applications.
摘要：
本研究描述了一个资源模块的开发，该模块是名为“NIGMSSandboxforCloud-basedLearning”（https://github.com/NIGMS/NIGMS-Sandbox）的学习平台的一部分。沙箱的整体起源在本补编开头的编辑NIGMS沙箱中进行了描述。该模块使用Nextflow以交互式格式提供有关从头转录组组装的学习材料，该格式使用适当的云资源进行数据访问和分析。云计算是一种强大的新手段，生物医学研究人员可以通过它访问以前无法实现或过于昂贵的资源和容量。为了利用这些资源，然而,生物医学研究界需要新的技能和知识。我们在这里介绍一个基于云的训练模块，与GoogleCloud共同开发，德勤咨询,和NIHSTRIDES计划,它使用从头转录组组装的生物学问题来演示和教授计算工作流（使用Nextflow）以及云服务的成本和资源高效使用（使用GoogleCloudPlatform）的概念。我们的工作强调了减少现场计算资源的必要性和基于云的基础设施对生物信息学应用的可访问性。
