UCSD, Yale Create Neuroscience Gateway

By Robert Gelber

August 14, 2012

A new partnership is underway as the University of California San Diego (UCSD) and Yale University have been awarded a grant to build a neuroscience gateway. The three-year, $805,000, NSF-funded endeavor goes by the unwieldy name: “Advanced Biological Informatics Development: Building a Community Resource for Neuroscientists.” While the moniker is quite a mouthful, the project aims to make neuroscience-based resources easily available to students and researchers.

brain imageThe partners have been tasked with delivering HPC storage and compute resources as a service for neurological researchers. The details of the grant call for the San Diego Supercomputing Center (SDSC) to build a software infrastructure, taking advantage of the existing Neuroscience Information Framework (NIF) project.

Part of the new service involves developing a Web portal, the Neuroscience Gateway (NSG), which allows researchers to upload models, manipulate HPC job parameters, store and retrieve data and view HPC job statuses.

SDSC researcher Amit Majumdar, principal investigator for the project, was quoted in an official statement saying:

This gateway will allow neuroscientists to use HPC resources without having to have detailed knowledge about the implementation of the codes on HPC resources, or know all the complexities of how supercomputers work.

One task envisioned for the portal includes computational modeling of cells and neural networks. The research is extremely compute intensive, requiring capacity typically found only in elite supercomputing centers. Students and scientists without local access to machines of this ilk will be able to reach them remotely through the service. According to Majumdar, the Neuroscience Gateway is slated to use the SDSC Cloud to store simulation results, “where they will be secure and easily accessed and shared.”

Compute capacity for the program will be provided by a collection of NSF supercomputing centers. These systems make up the Extreme Science and Engineering Discovery Environment (XSEDE) infrastructure and include some of the world’s fastest systems. The list is an unofficial who’s who of research facilities in the United States:

Blacklight – Pittsburgh Supercomputing Center

Forge – National Center for Supercomputing Applications

Gordon – San Diego Supercomputing Center

Kraken – National Institute for Computational Sciences

Lonestar – Texas Advanced Computing Center

Ranger – Texas Advanced Computing Center

Steele – Purdue University

Trestles – San Diego Supercomputing Center

Majumdar believes the specialized science portal will positively impact all researchers, but is especially significant for underserved groups that lack access to large HPC resources.

“Many of these investigators and students would otherwise find it very difficult, if not impossible, to implement and study models that press or exceed the storage and computing speed capabilities that are under their direct control,” he said.

The new service will most likely interface with the Neuroscience Information Network, a project that touts itself as the largest source of neuroscience tools and data on the Web. Maryann Martone, NIF principle investigator as well as co-principal investigator for the UC San Diego Neuroscience Gateway award, says the gateway will also act as a collaborative space where researchers can share their ideas and data.

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