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

University Of California-San Diego, La Jolla CA

Investigators

Abstract

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.