The University of California, at San Diego and Yale University have been awarded a collaborative grant by the National Science Foundation (NSF) to develop a Neuroscience Gateway (NSG) that gives neuroscientists broadened access to essential high-performance computing (HPC) and storage resources.
Under the UC San Diego grant, the university's San Diego Supercomputer Center (SDSC) and its Neuroscience Information Framework project will create a software infrastructure that can be used to make neuroscience-specific compute and software tools conveniently available to students and investigators.
The project, called "Advanced Biological Informatics Development: Building A Community Resource for Neuroscientists," will offer compute time to neuroscience users through a streamlined process using a simple web portal-based environment for uploading models, retrieving and storing data, and specifying the parameters for running high-performance computing (HPC)-based neuronal simulations, including querying the status and completion of various jobs. The NSG portal, which is under development, will be available at http://www.nsgportal.org/.
"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," said SDSC researcher Amit Majumdar, principal investigator for the collaborative award.
The project will enable members of the neuroscience community, including scientists, professors, and students, to use large HPC resources for research and instruction and to run leading simulation and analysis packages to perform tasks such as computational modeling of cells and large neural networks. This will benefit all students and researchers, especially those who lack access to HPC resources and are thus at a significant disadvantage compared to the very few who have it, by removing the barriers for progress for many including historically underrepresented groups.
"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," said Majumdar, who directs the scientific computing applications group at SDSC and is also part of UC San Diego's Department of Radiation Medicine and Applied Sciences.
Subha Sivagnanam and Kenneth Yoshimoto, both from SDSC and who have expertise in software engineering and parallel computing, will help develop the neuroscience gateway. They have been running performance studies of the neuronal simulation software NEURON on SDSC's Triton computer cluster, which has 256 nodes with 2 quad-core Intel- Nehalem processors with clock speed of 2.4 GHz (gigahertz) and 24 GB (gigabytes) of memory.
"Such a gateway will help advance research by lowering or eliminating the administrative and technical barriers that currently make it difficult for neuroscientists to use HPC resources," said Maryann Martone, principal investigator of the Neuroscience Information Framework (NIF) project, and co-principal investigator for the UC San Diego Neuroscience Gateway award. "This work aligns well with the NIF project which provides a portal into the largest source of neuroscience tools and data on the web and is housed in the Center for Research in Biological Systems (CRBS) at UC San Diego. The gateway will also provide a community forum for neuroscientists to collaborate and share their data."
NIF's Anita Bandrowski, a neuroscientist, and Vadim Astakhov, also a parallel computing expert, will help in designing and testing the gateway. Ted Carnevale, principal investigator of the Yale grant, and Michael Hines, both from the Neurobiology Department at the Yale School of Medicine, are also involved in this project. They are the developers of the NEURON software which will be available via the science gateway. Other neuronal software to be provided by the gateway includes GENESIS3, MOOSE, PyNN, and NEST.
"The past two decades have seen an accelerating growth in the use of computational modeling in neuroscience," said Carnevale. "It has also revealed a research bottleneck in terms of accessing and using cyberinfrastructure and there is a broad consensus that the wider computational neuroscience community needs easier access to complex cyberinfrastructure (CI) and HPC resources."
Specifically, the NSG architecture will transparently distribute user jobs to appropriate HPC resources provided by various NSF supercomputer centers. The HPC systems are part of the agency's Extreme Science and Engineering Discovery Environment (XSEDE), one of the most advanced, powerful, and robust collection of integrated advanced digital resources and services in the world.
The NSG team will also collaborate with developers of neural simulation software to optimally install, test, and benchmark these applications, and allow developers to test new versions before release. Project leaders will also target the promotion of the NSG to underrepresented minority scientists and minority serving institutions through active participation in summer training academies and a network of previously mentored female and minority students, some now employed at minority serving institutions.
Storing Larger Datasets in the SDSC Cloud