Lessons learned from Galaxy, a Web-based platform for high-throughput genomic analyses

2012 IEEE 8th International Conference on E-Science Pub Date : 2012-10-08 DOI:10.1109/ESCIENCE.2012.6404442

Jeremy Goecks, The Galaxy Team, A. Nekrutenko, James Taylor

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引用次数: 6

Abstract

High throughput sequencing assays have given rise to the field of genomics and transformed biomedical research into a computational science. Due to the large size of genomics datasets, high-performance computing is essential for analysis. Galaxy (http://galaxyproject.org) is a popular Web-based platform that can be used for all facets of genomic analyses, including data retrieval and integration, multi-step analysis, repeated analyses via workflows, visualization, collaboration, and publication. This paper describes Galaxy and discusses four lessons learned from the development of Galaxy. First, Galaxy uses open, extensible frameworks so that it can be adapted to new technologies as they become available. Second, by leveraging Web technologies, Galaxy makes genomics tools accessible to everyone and provides a common platform for collaboration. Third, Galaxy fosters community amongst both developers and users and encourages each community to adapt and extend Galaxy to meet their needs. Finally, Galaxy software development and genomic research are closely coupled, and challenges encountered during genomic research drive Galaxy development.

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从基于网络的高通量基因组分析平台Galaxy获得的经验教训

高通量测序技术使基因组学领域兴起，并将生物医学研究转变为计算科学。由于基因组数据集的庞大规模，高性能计算对于分析是必不可少的。Galaxy (http://galaxyproject.org)是一个流行的基于web的平台，可用于基因组分析的所有方面，包括数据检索和集成、多步骤分析、通过工作流重复分析、可视化、协作和发布。本文介绍了《银河》，并讨论了从《银河》的开发中得到的四点经验教训。首先，Galaxy使用开放的、可扩展的框架，这样它就可以适应新技术。其次，通过利用网络技术，银河使基因组学工具对每个人都可用，并提供了一个共同的合作平台。第三，Galaxy在开发者和用户之间建立社区，并鼓励每个社区调整和扩展Galaxy以满足他们的需求。最后，Galaxy软件开发与基因组研究紧密结合，基因组研究过程中遇到的挑战推动了Galaxy的发展。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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2012 IEEE 8th International Conference on E-Science

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