Science Portals & Science Gateways

A science portal or 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 save researchers and institutions both time and money.

A single portal or 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 portals and 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 Gateways Community Institute (SGCI)

Science gateways are web-based, community-developed interfaces that provide researchers with access to resources and tools that make it possible to run available applications on supercomputers such as Comet so results come quickly, even with large data sets. Browser access offered by such gateways allows researchers to focus on their scientific problem without having to learn the details of how supercomputers work. Gateways can be created and used by a diverse range of science domains, from the life sciences to digital humanities. Moreover, gateways should be economical to operate, scalable, and above all, sustainable as a resource for researchers.

In 2016, a collaborative team led by SDSC Associate Director Nancy Wilkins-Diehr was awarded a five-year, $15 million National Science Foundation (NSF) grant to establish a Science Gateways Community Institute (SGCI) to accelerate the development and application of highly functional, sustainable science gateways that address the needs of researchers across the full spectrum of NSF directorates and other federal agencies.

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.

In April 2018 SGCI was approved by an NSF review panel to move into the execution phase. SGCI has provided consulting or in-depth expertise to more than 65 projects and written over 100 letters of commitment for interested researchers in the first two-and-a-half years of the program. Proposals with SGCI support have enjoyed a 41% success rate. In mid-2019 Michael Zentner succeeded Wilkins-Diehr as the PI of SGCI, following Wilkins-Diehr’s retirement from SDSC. Zentner joined SDSC following nine years with Purdue University.

SGCI offers a full range of services and expertise including:

Building and Running Gateways

  • Software developers offer their expertise in building or enhancing an existing gateway in the areas of graphic design, cybersecurity, business and sustainability planning, and user engagement.
  • Free hosting allowing gateway builders to test frameworks.

Community Resources & Networking

  • A growing collections of searchable and browsable gateways.
  • A community forum to post questions and receive relevant information.
  • Other online resources including publications, case studies, and materials.
  • An annual Gateways Conference Series that lets developers and researchers interact and share their knowledge and gateways experiences.

Education and Training

  • SCGI Focus Weeks: A week-long workshop that teaches teams how to effectively design, build, and sustain science gateways.
  • Webinars: A rotating selection of topics of interest.
  • Student Programs and Engagement: Opportunities for students and faculty through workshops and internships, with a focus on assisting underrepresented groups and minority-serving institutions.

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, OpenTopography employs sophisticated cyberinfrastruc­ture that includes large-scale data management, distributed high-performance computing (HPC), and service-oriented architectures, providing researchers with efficient web-based access to large, high-resolution topographic datasets.

As of February 2019, OpenTopography data holdings comprise 283 lidar point cloud datasets with over 1.21 trillion lidar returns and 157 high-resolution raster datasets covering 219,648 km2, and six global datasets including the highly popular Satellite Radar Topography Mission (SRTM) global 30m dataset. OpenTopography has established itself as a resource that supports a broad interdisciplinary user base in academia and beyond. Since its initia­tion, over 86,801 unique users have run over 331,987 jobs via the gateway portal processing more than 5 trillion Lidar points. At least 290 peer-reviewed articles and other publications have been produced using OpenTo­pography resources. These include academic works in earth science, ecology, hydrology, geospatial and computer science, and engineering.

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).