CIBR: Collaborative Research: Providing sustainable Galaxy service on XSEDE resources

CIBR：协作研究：在 XSEDE 资源上提供可持续的 Galaxy 服务

• 批准号: 1929694
• 负责人: Anton Nekrutenko
• 金额: $ 203.55万
• 依托单位: Pennsylvania State Univ University Park
• 依托单位国家: 美国
• 项目类别: Continuing Grant
• 财政年份: 2019
• 资助国家: 美国
• 起止时间: 2019-12-15 至 2023-11-30
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1929694&HistoricalAwards=false
• 关键词: CIBR; Collaborative; Research; Providing; sustainable

Due to proliferation of high throughput sequencing and imaging techniques biology has become a de facto data-driven discipline. Yet the ability to take full advantage of these technological advances is still lagging for most biological researchers. The Galaxy Project started in 2005 to create a system enabling biologists without informatics expertise or local compute resources to perform computational analysis through the web. The main site located at the Texas Advanced Computing Center allows researchers to analyze data freely and access training materials on analytic approaches, their assumptions and limitations, and best practices. Galaxy combines the accessibility of GUI with infinite power of exploratory analyses provided by interactive environments. This combination empowers high quality research and, again, provides a robust launchpad for quantitative and data analysis training. The public instance of Galaxy is used by tens of thousands of registered users and performs between 300 to 500 thousands of analyses every month and has been cited in over 7,000 publications. This proposal aims at changing how Galaxy utilizes existing and procures additional infrastructure to put it on a sustainable footing going forward. The plan for achieving these goals involves two primary focal areas: The first objective is to adapt Galaxy architecture to take advantage of tiered storage. This will allow significantly reducing the cost and ensure effective management of storage infrastructure. Within this aim the team will develop and implement strategies for the management of existing data and leverage an existing policy-based system for controlling when and what data to move between tiers. The second objective is to design and implement functionality for "premium storage". The work undertaken within this aim will allow users with existing XSEDE allocations to "extend" their storage. Other users will be able to acquire additional Galaxy storage on TACC systems by paying for it directly. These changes will allow the Galaxy service to continue to provide a basic level of storage to all users while supporting a flexible set of options to scale beyond that level as needed. For more information about Galaxy visit the website at https://galaxyproject.org/.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.

由于高通量测序和成像技术的增殖，生物学已成为一种事实上的数据驱动学科。然而，充分利用这些技术进步的能力仍然落后于大多数生物学研究人员。 Galaxy项目始于2005年，目的是创建一个系统，使生物学家无信息专业知识或本地计算资源可以通过网络进行计算分析。位于德克萨斯州高级计算中心的主要站点使研究人员可以自由分析数据，并访问有关分析方法，其假设和局限性以及最佳实践的培训材料。 Galaxy将GUI的可及性与交互式环境提供的探索性分析的无限能力相结合。这种组合赋予了高质量的研究，并再次为定量和数据分析培训提供了强大的发射台。银河系的公共实例由成千上万的注册用户使用，每月进行300至50万分析，并在7,000多个出版物中引用。该提案旨在改变Galaxy如何利用现有的方式，并采购其他基础设施将其置于可持续的基础上。实现这些目标的计划涉及两个主要焦点领域：第一个目标是调整银河体系结构以利用分层的存储。这将大大降低成本并确保存储基础设施的有效管理。在此目标中，团队将制定和实施策略来管理现有数据，并利用现有的基于策略的系统来控制何时以及在层次之间移动哪些数据。第二个目标是设计和实施“高级存储”的功能。在此目标中进行的工作将使现有XSEDE分配的用户可以“扩展”其存储空间。其他用户将能够直接支付TACC系统上的其他Galaxy存储。这些更改将使Galaxy Service继续为所有用户提供基本的存储水平，同时支持一组灵活的选项，以根据需要扩展该级别。有关Galaxy的更多信息，请访问该网站https://galaxyproject.org/.this Award反映了NSF的法定任务，并使用基金会的知识分子优点和更广泛的影响审查标准，认为值得通过评估来获得支持。

项目成果

Scalable, accessible and reproducible reference genome assembly and evaluation in Galaxy

Galaxy 中可扩展、可访问且可重复的参考基因组组装和评估

• DOI: 10.1038/s41587-023-02100-3
• 发表时间: 2024
• 期刊: Nature Biotechnology
• 影响因子: 46.9
• 作者: Larivière, Delphine;Abueg, Linelle;Brajuka, Nadolina;Gallardo-Alba, Cristóbal;Grüning, Bjorn;Ko, Byung June;Ostrovsky, Alex;Palmada-Flores, Marc;Pickett, Brandon D.;Rabbani, Keon
• 通讯作者: Rabbani, Keon