CIPRES Awarded Two Federal Grants to Support Innovations in Biological Research

Published August 23, 2018

The CIPRES science gateway, which supports major discoveries about evolutionary relationships among our planet’s living creatures, has been awarded grants from the National Science Foundation (NSF) and the National Institutes of Health (NIH) that will provide more than $2.8 million to sustain and enhance the gateway.

CIPRES (CyberInfrastructure for Phylogenetic RESearch) gives biologists around the world access to sophisticated software tools that run on supercomputers supported by NSF’s eXtreme Science and Engineering Discovery Environment (XSEDE). Launched as a gateway in 2009 at the San Diego Supercomputer Center (SDSC) at UC San Diego, CIPRES allows users to solve significant research problems using tools and computing power that often are otherwise unavailable.

Science gateways provide browser interfaces that make it possible to analyze large data sets on supercomputers such as SDSC’s Comet, letting researchers focus on their scientific problem without having to learn the details of how supercomputers work and how to access and organize the data needed. Using CIPRES, researchers can also analyze their data while working in the field, and because there is no charge, individuals can contribute to our understanding of life on earth independent of the resources at their home institutions.

This year CIPRES will support more than 10,000 researchers who are investigating a wide range of questions about life on earth, including:

• How do viruses and bacteria mutate through time, and how can we use this information to understand and control disease outbreaks?
• How many species are there are on earth, and how do they work together to create functional ecosystems?
• Are insects that look identical to each other actually from the same species?
• How do animals evolve and change in response to their environment?
• How can we preserve more vulnerable species in a time of climate change?

Results of investigations conducted using CIPRES have been documented in at least 4,500 peer-reviewed publications, including some of science’s most prestigious journals such as Nature, Cell, Science, and Proceedings of the National Academy of Sciences (PNAS).

“Understanding the evolutionary history of living organisms is a central goal of nearly every discipline in biology,” said SDSC Bioinformatics Researcher Mark Miller, the gateway’s principal investigator. “Right now, discoveries in evolutionary biology depend on access to powerful computers. CIPRES’s wide adoption by the biological community underscores the importance of this resource to the future of biological research.

“The awards we received from NSF and NIH show that these agencies understand the importance of CIPRES to research in pure biology and in biomedicine,” he added. “The awards give us the opportunity to make CIPRES an even better resource.”

“Our goal is to enhance researcher productivity by providing phylogenetics and population genetics tools optimized to run on supercomputers,” said Wayne Pfeiffer, an SDSC Distinguished Scientist and the project’s co-principal investigator. “These tools let researchers solve problems in days that would otherwise take weeks or even months.”

The NSF award stems from a program that provides funds to sustain the operations of online resources while project personnel seek funding elsewhere to add new features and capabilities. This award will provide about $1 million over three years to sustain CIPRES operations, ensuring that biologists who have come to rely on CIPRES can continue their work uninterrupted.

The NIH award provides $1.86 million over four years to develop and release new capabilities for users. The CIPRES project team will use these funds to improve the gateway’s usability, improve the efficiency of user experience, allow users to work more collaboratively, and provide access to cloud computing beyond what is available currently through the XSEDE program.

About SDSC

As an Organized Research Unit of UC San Diego, SDSC is considered a leader in data-intensive computing and cyberinfrastructure, providing resources, services, and expertise to the national research community, including industry and academia. Cyberinfrastructure refers to an accessible, integrated network of computer-based resources and expertise, focused on accelerating scientific inquiry and discovery. SDSC supports hundreds of multidisciplinary programs spanning a wide variety of domains, from earth sciences and biology to astrophysics, bioinformatics, and health IT. SDSC’s petascale Comet supercomputer is a key resource within the National Science Foundation’s XSEDE (Extreme Science and Engineering Discovery Environment) program.