Democratization of Data Analysis in Life Sciences Through Galaxy

描述（申请人提供）：生物医学研究已迅速转变为一门信息学密集型学科。这在许多层面上带来了挑战，从计算基础设施和专业知识的可用性，跟上快速发展的工具和最佳实践的负担，实验人员和计算研究人员之间的沟通困难，以及确保再现性的困难。在过去的六年里，我们开发了一个开源软件框架Galaxy （http://usegalaxy.org）来解决这些问题。Galaxy提供了一个可访问的分析环境，允许实验人员在大型数据集上使用尖端工具，并具有自动跟踪以确保再现性。Galaxy使工具开发人员可以轻松地将他们的工具快速地交到实验人员手中。银河已经成为基因组研究界不可或缺的资源。首先，成千上万的实验家在他们的研究中使用了Galaxy的工具（正如许多出版物所证明的那样）。除此之外，Galaxy已被许多实验室和研究所采用为本地分析基础设施。Galaxy足够灵活，可以部署在各种不同的计算资源上，这在数据生产日益分散的情况下尤为重要。Galaxy的核心是一个强大的可扩展框架，其他重要的社区资源项目正在对其进行集成或构建。因此，Galaxy的理想定位是成为共享和交流分析的基础。我们建议在一个分散的世界中，用新的方法来扩展银河资源，以实现可访问、透明和可重复的分析。在生物项目的推动下，我们将为几个基于测序的实验建立最佳实践工作流程。我们将创造创新的方法来自动化打包和部署分析工具。我们将建立并维护Galaxy Tool Shed，一个共享工具、最佳实践工作流和分析策略的中心。我们将开发一种新的方法来发表分析。我们将利用现有的Galaxy Tools创建一个可视化分析框架。最后，我们将建立一个完整的解决方案来管理测序工作流程，包括样品跟踪和仪器集成。

DESCRIPTION (provided by applicant): Biomedical research has been rapidly transformed into an informatics intensive discipline. This has created challenges at many levels, from the availability of computational infrastructure and expertise, the burden of keeping up with rapidly developing tools and best-practices, communication difficulties between experimentalists and computational researchers, and difficulties ensuring reproducibility. Over the last six years we have developed an open-source software framework, Galaxy (http://usegalaxy.org), to address these issues. Galaxy provides an accessible analysis environment allowing experimentalists to use cuttingedge tools on large datasets, with automated tracking to ensure reproducibility. Galaxy makes it easy for tool developers to quickly put their tools into experimentalist's hands. Galaxy has become an indispensable resource for the genomic research community. First, for the thousands of experimentalists using Galaxy's tools in their research (as evidenced in many publications). Beyond that, Galaxy has been adopted as the local analysis infrastructure for many dozens of labs and institutes. Galaxy is flexible enough to be deployed on a variety of different compute resources, particularly important as data-production is increasingly de-centralized. At Galaxy's core is a powerful extensible framework that other important community resource projects are now integrating or building on. Thus Galaxy is ideally positioned to become a substrate for sharing and communicating analysis. We propose to expand the Galaxy resource with novel approaches for accessible, transparent, and reproducible analysis in a decentralized world. Driven by biological projects, we will build best practice workflows for several sequencing based experiments. We will create innovative methods to automate packaging and deploying analysis tools. We will build and maintain the Galaxy Tool Shed, a hub for sharing tools, best-practice workflows, and analysis strategies. We will develop a novel approach for publishing analysis. We will create a framework for visual analytics leveraging existing Galaxy Tools. Finally, we will build a complete solution for managing sequencing workflows including sample tracking and instrument integration.