Embedding CIPRES science gateway capabilities in phylogenetics software environments

Authors:
Mark A. Miller;Terri Schwartz;Wayne Pfeiffer
Affiliations:
University of California, San Diego, La Jolla, CA;University of California, San Diego, La Jolla, CA;University of California, San Diego, La Jolla, CA
Venue:
Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery
Year:
2013

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Abstract

The explosive growth in DNA sequence data over the past decade makes it possible to clarify evolutionary relationships among all living things at an unprecedented level of resolution. Phylogenetic inference codes are computationally intensive, so turning this wealth of DNA sequence data into new insights about evolution requires access to high performance computing (HPC) resources. The CIPRES Science Gateway (CSG) was designed to meet this need by providing browser-based access to phylogenetic codes run on XSEDE compute resources. The CSG has lowered the barrier for access to HPC resources for biologists worldwide, supporting more than 6,100 users and enabling more than 600 publications over the past three years. Here we describe plans to create a new set of public CSG web services that can be accessed by any developer through a programmatic interface. These services will allow us to embed access to XSEDE resources within well-established phylogenetics software packages, thus leveraging the investments by developers in creating these rich work environments and by users in learning to use them. The services will also allow any developer with modest scripting skills to access and use CSG capabilities outside of the current browser interface. Our goal in creating these services is to allow scientists to conduct analyses without leaving their preferred work environment, whether that is a complex desktop application, a set of ad hoc scripted workflows, or the existing CSG browser interface. This paper describes the architectural design of the CSG web services, identifies potential issues that will be addressed in exposing programmatic access to HPC resources, and describes plans to embed the CSG web services in eight popular community applications.