Science Portals / Gateways

A Science Gateway is a community-developed set of tools, applications, and data that are integrated through a web-based portal or a suite of applications. They provide scientists with access to many of the tools used in cutting-edge research – telescopes, seismic shake tables, supercomputers, sky surveys, undersea sensors, and more. Such gateways connect often diverse resources and make them easily accessible in ways that saves researchers and institutions both time and money.

A single gateway can give thousands of users access to current, optimized versions of analysis codes at any time. Codes with a large user base can be used by thousands of scientists through a single installation, rather than through hundreds of local installations. Researchers can focus on their scientific goals without having to know how supercomputers and other data cyberinfrastructures work. Gateways also help foster collaborations and the exchange of ideas among researchers.

Science gateways have shown tremendous growth in terms of the number of users, the number of processing hours used on HPC resources by the broader user community, and in the number of published research papers enabled. Gateways can also be readily used for teaching classes, workshops, and tutorials without having to set up codes on HPC resources, or create new accounts for students/attendees.

Science Gateway Institute

SDSC has been a leader in developing Science Gateways for a wide range of research communities. In 2012, SDSC was named the lead institution on an NSF planning grant for a conceptualization phase of a Science Gateway Institute that would offer a complete range of services aimed at connecting numerous individual groups developing domain-specific, user-friendly, Web-based portals and tools that enable scientific research. Partner institutions include Elizabeth City State University; Indiana University; Purdue University; the Texas Advanced Computing Center (TACC) at The University of Texas, Austin; and the University of Michigan, Ann Arbor.

Through a one-year, $500,000 conceptualization award, the team developed a strategic plan for a much larger Science Gateway Institute as part of the NSF’s Software Institutes program. If funded, the Institute would provide a full support system for those developing gateways – from technical expertise to licensing advice to long-term planning and project management.

“Sharing expertise about basic infrastructure allows developers to concentrate on the novel, the challenging, and the cutting-edge development needed by their specific user community,” said Nancy Wilkins-Diehr, SDSC associate director and principal investigator on the project.

The team envisions the Science Gateways Institute as offering a startup, or incubation service, which would include complete development environment and hosting service, as well as consulting, documentation, and software recommendations to ensure the gateway is properly planned for maximum participation and success. An extended support team could build gateways for research teams that request support, transferring knowledge by teaching those teams what it takes to build, enhance, and operate gateways in the process. A 29,000-person survey of NSF principal investigators, university administrators and others showed overwhelming interest in such services.

CIPRES

In 2013 SDSC received a three-year, $1.5 million award from the National Science Foundation (NSF) to make access to supercomputing resources simpler and more flexible for phylogenetics researchers. The award, which follows an earlier NSF grant that ran from 2003 to 2008, is for the CIPRES Science Gateway, a web site that allows researchers to explore evolutionary relationships between species using supercomputers provided by the NSF XSEDE project. CIPRES stands for CyberInfrastructure for Phylogenetic REsearch, and is among the most popular gateways in the XSEDE community. The CIPRES Gateway allows scientists to conduct their research in significantly shorter times without having to understand how to operate supercomputers, according to Mark Miller, principal investigator of the CIPRES gateway and an SDSC biologist.

To date, the CIPRES Science Gateway has supported more than 12,000 users and has led to more than 1,300 publications of phylogenetic studies involving species in every branch of the Tree of Life.

Neuroscience Gateway

UC San Diego and Yale University are currently working under a collaborative NSF grant called “Advanced Biological Informatics Development: Building A Community Resource for Neuroscientists” to develop a Neuroscience Gateway (NSG) that gives neuroscientists broadened access to essential high-performance computing resources. The Neuroscience Gateway (NSG) is a science gateway software infrastructure that makes neuroscience-specific computational tools conveniently available to researchers and students. The NSG offers high-performance compute time to neuroscience users through a streamlined process using a simple web portal-based environment for uploading neuronal models, running neuronal simulations on XSEDE’s HPC resources, querying the status of jobs, and retrieving and storing output results. SDSC’s Amit Majumdar, PI of the NSF grant along with Yale PI Ted Carnevale, have seen tremendous adoption of NSG by the computational neuroscientists whose computing needs for simulation of large and complex brain models exceeds the resources available within their labs or institutions. NSG has been in production since early 2013 and within the first two years has provided over 3 million core hours to computational neuroscientists on SDSC’s Trestles cluster.

OpenTopography

Initiated in 2009 with funding from the NSF, OpenTopography provides easy access to earth science-oriented, high-resolution topographical data and processing tools for a broad spectrum of research communities. A collaboration between UC San Diego, Arizona State University and UNAVCO (a non-profit university-governed consortium that facilitates geoscience research and education), OpenTopography – based at SDSC – employs sophisticated cyberinfrastructure that includes large-scale data management, high-performance computing, and service-oriented architectures, providing researchers with efficient Web-based access to large, high-resolution topographic datasets. As of June 2016, OpenTopography's growing data holdings included 195 Lidar (for Light Detection and Ranging) point cloud datasets (>843 billion points) covering 181,436 km2.  More than 11,870 registered users and tens of thousands of anonymous guest users have run 63,977 point cloud jobs, accessing more than 2.7 trillion Lidar points, resulting in more than 151 peer-reviewed publications.

SciGaP

Under a 2013 NSF award totaling $5 million for a collaborative five-year project, SDSC researchers are helping to develop and build a Science Gateway Platform (SciGaP) as a service to advance scientific discovery by providing researchers improved access to a variety of hosted or cloud services. The project is being led by Indiana University’s (IU) Marlon Pierce and Suresh Marru. The SciGaP project will create a set of hosted infrastructure services that gateway providers can easily adopt to build new gateways, according to Amit Majumdar, director of SDSC’s Data Enabled Scientific Computing (DESC) group. These services will provide the basic features that any gateway requires, such as tools to connect high-performance computers and data resources across the country. Majumdar and Mark Miller of SDSC are leading SDSC’s participation in the project. Also participating in the project is Borries Demeler from The University of Texas Health Science Center at San Antonio (UTHSCSA).