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UC San Diego, Yale to Build Neuroscience Gateway

Neuron illustration (NIH)

(National Institute on Aging, NIH)

University of California in San Diego and Yale University are developing an online gateway to provide high-performance computational tools for neuroscientists. The Neuroscience Gateway project is funded by a three year, $707,000 grant from National Science Foundation.

UC San Diego will make available its supercomputer center and Neuroscience Information Framework for neuroscientists to access advanced computational software and tools. The Neuroscience Gateway will offer computing time through a Web-based portal for uploading models, retrieving and storing data, and specifying variables and conditions in high-performance computing-based neuronal simulations.

The portal is expected to offer neuroscientists and students high-performance computing (HPC) resources for research and instruction and to run leading simulation and analysis packages performing tasks such as computational modeling of cells and large neural networks. “This gateway will allow neuroscientists to use HPC resources,” says Amit Majumdar, principal investigator on the project, “without having to have detailed knowledge about the implementation of the codes on HPC resources, or know all the complexities of how supercomputers work.”

The Neuroscience Gateway architecture takes advantage of UC San Diego’s participation in the Extreme Science and Engineering Discovery Environment (XSEDE), an initiative of National Science Foundation that links 16 supercomputers and high-end visualization and data analysis resources across the country. The gateway, says its developers, will be able to transparently distribute user jobs to appropriate high-performance computing resources provided by XSEDE member supercomputer centers.

In addition, Neuroscience Gateway makes use of the San Diego supercomputer’s cloud storage services, called SDSC Cloud, to store the results of large neuronal simulations. “The idea is to move the output files produced on various HPC resources to the SDSC Cloud where they will be secure and easily accessed and shared,” says Majumdar.

The Neuroscience Gateway aims to recruit developers of neural simulation software to install, test, and benchmark these applications, and allow developers to test new versions before release. The gateway staff will also reach out to underrepresented minority scientists and minority serving institutions with summer training academies and a network of previously mentored female and minority students, some now employed at minority serving institutions.

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