The University of California, San Diego (La Jolla, CA) has received an ABI development award to create the CIPRES REST API (CRA), a set of enabling public web services for the biology community. The CRA will make it possible for any biologist with modest programming skills to access and run powerful phylogenetic tools on NSF XSEDE supercomputers from within their preferred work environment. The project will embed the CRA into eight distinct software environments that are widely used in the biology community, providing direct access to supercomputing resources from within these familiar working environments. The CRA will make it possible for scientists to analyze much larger data sets than is currently possible without changing their normal work environment or learning to use new software. Community developers will be able to incorporate the CRA tools into their software environments in new and creative ways. The tools created by this project are an extension of the prototype CIPRES Science Gateway, a web application that allows researchers to run large phylogenetic analyses on NSF XSEDE computing resources through a standard browser interface. In its first 30 months of operation, the CIPRES Science Gateway has run analyses for more than 5,000 users, enabled 400+ scholarly publications in biological disciplines ranging from Ecology to Virology, and was used by at least 68 instructors for curriculum delivery.
The impact of CIPRES Science Gateway prototype has been profound because understanding the evolutionary history of living organisms is central to all fields of biological research, and evolutionary relationships are explored primarily by comparing DNA and protein sequences using computationally intensive algorithms. The rate of DNA and protein sequence acquisition is currently increasing more rapidly than Moore's law. While this represents an unprecedented opportunity to clarify evolutionary relationships, it also means routine analyses can no longer be conducted with laptop/desktop computers. Researchers must have easy access to high performance computing (HPC) resources to participate in the discovery process. The CRA will improve the efficiency of access to computational resources by shifting from the rigid browser paradigm of the CIPRES Science Gateway to a pervasive access model, where the phylogenetic tools required for modern biological research are available from within the researcher's preferred environment. The software and techniques created will be completely generic and easily adapted to any area of science where progress is limited by access to computational resources. More information about this project can be obtained from www.phylo.org/index.php/portal/ or mmiller@sdsc.edu.
