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

了解地球上生命的进化在现代生物学的几乎每一个领域都是至关重要的。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。从进化研究获得的信息为农业和医疗政策提供信息，这两个领域对国家和全球经济的潜在影响是巨大的。目前，进化研究在很大程度上依赖于对大量DNA序列数据的分析。序列数据的系统发育分析和种群遗传学研究是计算密集型的，通过访问强大的高性能计算资源可以最有效地完成。该项目将维持CIPRES科学网关的运行，这是一项用于分析序列数据的首屈一指的网络服务，已为世界各地的30,000名研究人员提供了免费访问高性能计算机的便利条件。CIPRES允许个人研究人员和多个国家研究团队在任何可以连接到互联网的地方分析他们的数据，而且对于几乎不了解高性能计算的研究人员来说，它使运行分析尽可能容易。CIPRES运行的分析会产生比笔记本电脑更快的结果10&amp；#8208；到&amp；100&amp；。因此，全面的研究可以更快地完成，而在笔记本电脑上不实用的大型研究现在可以成功完成。CIPRES因此极大地提高了研究人员的生产力，并使高性能计算的普及，使研究人员能够独立于当地资源，为日益增长的对地球进化的理解做出贡献。CIPRES对发现速度的影响是巨大的；自2010年以来，它支持了4500多项已发表的研究研究，并已被90名教师在课堂环境中使用。CIPRES目前每年支持10,000名研究人员，他们正在调查蛋白质、病毒、细菌、植物和动物的进化史；识别新的属和物种；评估和开发新技术；以及探索不同种群的进化史。该项目将通过下列活动为这些研究人员维持CIPRES的持续在线存在：提供当前版本的社区系统发育和种群遗传学代码的浏览器和RESTful访问；NSF XSEDE项目单独支持的性能计算资源；更新代码和/或使用策略以帮助用户进行更多计算量大的分析；调整代码和策略以适应现有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能力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进行的作业的负面影响；通过在专业会议上发言和举办讲习班提供外联，以改善与系统学界的联系；监测使用情况统计数据，以更好地了解和提高CIPRES的效力；并争取超级计算机资源的分配，以支持CIPRES的大型用户群。该项目还将支持CIPRES工作台框架，这是一个支撑CIPRES的开源软件包，已被其他四个生物界采用，以创建自己的网关。CIPRES可通过http://www.phylo.org.This获得，该奖项反映了国家科学基金会的法定使命，并通过使用基金会的智力优势和更广泛的影响审查标准进行评估，被认为值得支持。

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.