ABI Sustaining: The CIPRES Science Gateway, a Resource for Biological Research

ABI 维持：CIPRES 科学网关，生物研究资源

• 批准号: 1759844
• 负责人: Mark Miller
• 金额: $ 101.19万
• 依托单位: University of California-San Diego
• 依托单位国家: 美国
• 项目类别: Standard Grant
• 财政年份: 2018
• 资助国家: 美国
• 起止时间: 2018-08-15 至 2022-07-31
• 项目状态: 已结题
• 来源: https://www.nsf.gov/awardsearch/showAward?AWD_ID=1759844&HistoricalAwards=false
• 关键词: ABI; Sustaining; CIPRES; Science; Gateway

Understanding the evolution of life on earth is of fundamental importance in virtually every field of modern biology. The study of evolutionary relationships helps researchers understand and respond to the origin and spread of viruses, develop strategies to preserve existing species, mitigate the impact of invasive species, and determine how environmental changes impact populations, shaping local and global ecologies. The information obtained from evolutionary research informs both agricultural and medical policies, two areas where the potential impact on national and global economies is substantial. At present, evolutionary research is critically dependent on the analysis of large amounts of DNA sequence data. Phylogenetic analyses and population genetics studies of sequence data are computationally intensive and are accomplished most efficiently through access to powerful high performance computing resources. This project will sustain the operation of the CIPRES Science Gateway, a premiere web service for analyzing sequence data that has provided 30,000+ researchers around the world with easy access to high‐performance computers at no charge. CIPRES lets individual investigators and multi‐national research teams analyze their data anywhere an internet connection is available, and it makes running the analyses as easy as possible for researchers with little knowledge of high‐performance computing. Analyses run by CIPRES produce results 10‐to‐100‐fold faster than is possible on a laptop computer. As a result, comprehensive studies can be completed more quickly, and large studies that are not practical on laptop computers can now be completed successfully. CIPRES thus dramatically improves researcher productivity and democratizes access to high‐performance computing, allowing investigators to contribute to the growing understanding of evolution on earth, independent of their local resources. The impact of CIPRES on the rate of discovery has been substantial; it has supported more than 4,500 published research studies since 2010 and has been used by 90+ instructors in classroom environments. CIPRES currently supports 10,000+ researchers annually who are investigating the evolutionary history of proteins, viruses, bacteria, plants, and animals; identifying new genera and species; evaluating and developing new techniques; and exploring the evolutionary history of diverse populations. This project will sustain the continued online presence of CIPRES for these researchers through the following activities: provide browser and RESTful access to current versions of community phylogenetics and population genetics codes deployed on high‐performance computing resources supported separately by the NSF XSEDE project; update the codes and/or usage policies to help users do more computationally demanding analyses; adapt the codes and policies to changes in available XSEDE resources and the local operating environment; modify the underlying software to support new code capabilities and correct any functionality or usability issues that arise; minimize negative impacts of planned and unplanned system outages on hundreds of simultaneous jobs; provide outreach by making presentations at professional meetings and hosting workshops to improve connection with the systematics community; monitor usage statistics to better understand and improve the effectiveness of CIPRES; and procure allocations of supercomputer resources to support the large CIPRES user community. The project will also sustain the CIPRES Workbench Framework, an open source software package that underlies CIPRES and that has been adopted by four other biology communities to create their own gateways. CIPRES can be accessed at http://www.phylo.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.

了解地球上生命的进化对于现代生物学的几乎每个领域都至关重要。进化关系的研究有助于研究人员了解和应对病毒的起源和传播，制定保护现有物种的策略，减轻入侵物种的影响，并确定环境变化如何影响种群，塑造当地和全球生态。从进化研究中获得的信息为农业和医疗政策提供了信息，这两个领域对国家和全球经济的潜在影响是巨大的。目前，进化研究严重依赖于对大量DNA序列数据的分析。序列数据的系统发育分析和群体遗传学研究是计算密集型的，并且通过访问强大的高性能计算资源最有效地完成。该项目将维持 CIPRES Science Gateway 的运行，CIPRES Science Gateway 是一项用于分析序列数据的首要网络服务，为全球 30,000 多名研究人员提供了免费轻松访问高性能计算机的服务。 CIPRES 允许个人研究人员和跨国研究团队在任何有互联网连接的地方分析他们的数据，并且对于对高性能计算知之甚少的研究人员来说，它可以尽可能轻松地运行分析。 CIPRES 运行的分析产生结果的速度比笔记本电脑快 10 到 100 倍。因此，可以更快地完成综合研究，并且现在可以成功完成笔记本电脑上不可行的大型研究。因此，CIPRES 极大地提高了研究人员的工作效率，并使高性能计算的访问变得民主化，使研究人员能够为加深对地球进化的理解做出贡献，而不受当地资源的影响。 CIPRES 对发现率的影响是巨大的；自 2010 年以来，它已支持超过 4,500 项已发表的研究，并已被 90 多名教师在课堂环境中使用。 CIPRES 目前每年为 10,000 多名研究人员提供支持，他们正在研究蛋白质、病毒、细菌、植物和动物的进化史；鉴定新属和新种；评估和开发新技术；并探索不同种群的进化历史。该项目将通过以下活动为这些研究人员维持 CIPRES 的持续在线存在：提供浏览器和 RESTful 访问，以访问当前版本的群落系统发育和群体遗传代码，这些代码部署在由 NSF XSEDE 项目单独支持的高性能计算资源上；更新代码和/或使用策略，以帮助用户进行计算要求更高的分析；使规范和政策适应可用 XSEDE 资源和本地操作环境的变化；修改底层软件以支持新的代码功能并纠正出现的任何功能或可用性问题；最大限度地减少计划内和计划外系统中断对数百个同时作业的负面影响；通过在专业会议上做演讲和举办研讨会来提供外展活动，以改善与系统学界的联系；监控使用统计数据，以更好地了解和提高 CIPRES 的有效性；并获取超级计算机资源的分配以支持大型 CIPRES 用户社区。该项目还将支持 CIPRES 工作台框架，这是一个开源软件包，是 CIPRES 的基础，并已被其他四个生物学社区采用来创建自己的网关。 CIPRES 可以通过 http://www.phylo.org 访问。该奖项反映了 NSF 的法定使命，并且通过使用基金会的智力价值和更广泛的影响审查标准进行评估，被认为值得支持。