Subhashini Sivagnanam

Subhashini Sivagnanam
San Diego Supercomputer Center

About

30
Publications
2,901
Reads
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330
Citations
Citations since 2016
20 Research Items
316 Citations
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20162017201820192020202120220204060
20162017201820192020202120220204060

Publications

Publications (30)
Article
To preserve scientific data created by publicly and/or philanthropically funded research projects and to make it ready for exploitation using recent and ongoing advances in advanced and large-scale computational modeling methods, publicly available data must use in common, now-evolving standards for formatting, identifying and annotating should sha...
Conference Paper
Full-text available
Biophysically detailed modeling provides an unmatched method to integrate data from many disparate experimental studies, and manipulate and explore with high precision the resultin brain circuit simulation. We developed a detailed model of the brain motor cortex circuits, simulating over 10,000 biophysically detailed neurons and 30 million synaptic...
Preprint
Full-text available
Biophysically detailed modeling provides an unmatched method to integrate data from many disparate experimental studies, and manipulate and explore with high precision the resulting brain circuit simulation. We developed a detailed model of the brain motor cortex circuits, simulating over 10,000 biophysically detailed neurons and 30 million synapti...
Article
Full-text available
EEGLAB signal processing environment is currently the leading open-source software for processing electroencephalographic (EEG) data. The Neuroscience Gateway (NSG, nsgportal.org) is a web and API-based portal allowing users to easily run a variety of neuroscience-related software on high-performance computing (HPC) resources in the U.S. XSEDE netw...
Conference Paper
Data sharing is an integral component of research and academic publications, allowing for independent verification of results. Researchers have the ability to extend and build upon prior research when they are able to efficiently access, validate, and verify the data referenced in publications. Despite the well known benefits of making research dat...
Conference Paper
The Neuroscience Gateway (NSG) is a science gateway that provides neuroscience researchers with tools on National Science Foundation high performance computing (HPC) platforms. The capability of NSG to accept not just static data for processing, but also user code to be compiled and executed, requires a user vetting process. In order to provide an...
Article
Full-text available
Computational models are powerful tools for exploring the properties of complex biological systems. In neuroscience, data-driven models of neural circuits that span multiple scales are increasingly being used to understand brain function in health and disease. But their adoption and reuse has been limited by the specialist knowledge required to eva...
Chapter
In this paper we analyze the performance of the computational neuroscience tool NEURON on Intel Knights Corner processors. Knights Corner was the many core processor that was followed by Knights Landing processors. NEURON is a widely used simulation environment for modeling individual neurons and network of neurons. NEURON is used to simulate large...
Conference Paper
Full-text available
The EEGLAB signal processing environment is a widely used open source software environment for processing electroencephalographic (EEG) data. The Neuroscience Gateway (nsgportal.org) is a software portal allowing users to readily run a variety of neuroimaging software on high performance computing (HPC) resources. We have expanded the current Neuro...
Conference Paper
The NSF funded Neuroscience Gateway (NSG) has been in operation since the early 2013. We originally designed NSG to reduce technical and administrative barriers that exist to using high performance computing resources for computational neuroscientists. In the last two years, in addition to computational neuroscientists, cognitive and experimental n...
Preprint
Full-text available
Computational models are powerful tools for investigating brain function in health and disease. However, biologically detailed neuronal and circuit models are complex and implemented in a range of specialized languages, making them inaccessible and opaque to many neuroscientists. This has limited critical evaluation of models by the scientific comm...
Conference Paper
Science Gateways provide user environments and a set of supporting services that help researchers make effective and enhanced use of a diverse set of computing, storage, and related resources. Gateways provide the services and tools users require to enable their scientific exploration, which includes tasks such as running computer simulations or pe...
Article
Full-text available
Biomimetic simulation permits neuroscientists to better understand the complex neuronal dynamics of the brain. Embedding a biomimetic simulation in a closed-loop neuroprosthesis, which can read and write signals from the brain, will permit applications for amelioration of motor, psychiatric, and memory-related brain disorders. Biomimetic neuroprost...
Conference Paper
In this paper, we first present a brief summary of the Neuroscience Gateway (NSG) which has been in operation since 2013. NSG is providing computational neuroscientists access to Extreme Science and Engineering Discovery Environment (XSEDE) high performance computing (HPC) resources. As a part of running the NSG we have interacted closely with the...
Poster
We present the Neuroscience Gateway (NSG), which allows neuroscientists to easily use High Performance Computing (HPC) resources for computationally intensive modeling tasks such as simulating large-scale networks or exploring high-dimensional parameter spaces. Potential HPC users typically face a high entry barrier because of numerous complex side...
Article
Here we describe the CIPRES Workbench (CW), an open source software framework for creating new science gateways with minimal overhead. The CW is a web application that can be deployed on a modest server, and can be configured to submit command line instructions to any resource where the application has submission privileges. It is designed to be hi...
Article
Full-text available
We present the Neuroscience Gateway (NSG) Portal http://www.nsgportal.org/, which we are developing so that neuroscientists can easily use High Performance Computing (HPC) resources for computationally intensive modeling tasks such as simulating large-scale networks or exploring high-dimensional parameter spaces. Potential users of HPC resources ty...
Article
Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers, and for developers to objectively benchmark their codes. Moreover, it is quite often to see repeated efforts spent on developing low-quality GP...
Article
The last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyber infrastructure to manage computational workflow and data. The neuronal simulation tools, used in t...
Conference Paper
In this paper, we describe the neuroscience gateway (NSG), which facilitates access to high performance computing resources for computational neuroscientists. Through a simple web-based portal, the NSG provides a streamlined environment for uploading models, specifying HPC job parameters, querying running job status, receiving job completion notice...
Article
Purpose: Graphics Processing Unit (GPU) has become increasingly important in radiotherapy. However, it is still difficult for general clinical researchers to access GPU codes developed by other researchers with GPU expertise, and also for developers to benchmark their codes. It is quite often to see repeated efforts spent on developing GPU codes wi...
Article
Last few decades have seen the emergence of computational neuroscience as a mature field where researchers are interested in modeling complex and large neuronal systems and require access to high performance computing machines and associated cyberinfrastructure to manage computational workflow and data. The neuronal simulation tools, used in this r...
Article
On a grid of computers, users often must decide between individual machines for job submission. Usually, the goal is to minimize time-to-completion. Several tools are available on TeraGrid to help users make this decision. In this paper, we use these tools to perform actual job submissions on TeraGrid machines. We evaluate the time-to-job-start eff...

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