research-article

A neuroscience gateway: software and implementation

Authors:

Subhashini Sivagnanam,

Anita BandrowskiAuthors Info & Claims

XSEDE '13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery

Article No.: 31, Pages 1 - 3

https://doi.org/10.1145/2484762.2484816

Published: 22 July 2013 Publication History

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Abstract

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 notices, and storing and retrieving output data. The NSG architecture transparently distributes user jobs to appropriate HPC resources available through the XSEDE organization.

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http://neuralensemble.org/PyNN/

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N. Wilkins-Diehr, D. Gannon, G. Klimeck, S. Oster, S. Pamidighantam, "TeraGrid Science Gateways and Their Impact on Science", IEEE Computer, Volume 41, Number 11 (November, 2008), pages 32--41.

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http://www.nsgportal.org

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M. Miller, W. Pfeiffer, and T. Schwartz, "CIPRES Science Gateway: A Community Resource for Phylogenetic Analyses," TeraGrid'11, July 18--21, Salt Lake City, 2011.

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Cited By

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Mohácsi MTörök MSáray STar LFarkas GKáli S(2024)Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software frameworkPLOS Computational Biology10.1371/journal.pcbi.101203920:12(e1012039)Online publication date: 23-Dec-2024
https://doi.org/10.1371/journal.pcbi.1012039
Inibhunu HMoradi Chameh HSkinner FRich SValiante T(2023)Hyperpolarization-Activated Cation Channels Shape the Spiking Frequency Preference of Human Cortical Layer 5 Pyramidal Neuronseneuro10.1523/ENEURO.0215-23.202310:8(ENEURO.0215-23.2023)Online publication date: 11-Aug-2023
https://doi.org/10.1523/ENEURO.0215-23.2023
Delorme A(2023)EEG is better left aloneScientific Reports10.1038/s41598-023-27528-013:1Online publication date: 9-Feb-2023
https://doi.org/10.1038/s41598-023-27528-0
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Index Terms

A neuroscience gateway: software and implementation
1. Information systems
  1. Information retrieval
  2. Information storage systems

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Published In

XSEDE '13: Proceedings of the Conference on Extreme Science and Engineering Discovery Environment: Gateway to Discovery

July 2013

433 pages

ISBN:9781450321709

DOI:10.1145/2484762

General Chair:
Nancy Wilkins-Diehr
San Diego Supercomputer Center

Permission to make digital or hard copies of part or all of this work for personal or classroom use is granted without fee provided that copies are not made or distributed for profit or commercial advantage and that copies bear this notice and the full citation on the first page. Copyrights for third-party components of this work must be honored. For all other uses, contact the Owner/Author.

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Association for Computing Machinery

New York, NY, United States

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Published: 22 July 2013

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XSEDE '13

XSEDE '13: Extreme Science and Engineering Discovery Environment: Gateway to Discovery

July 22 - 25, 2013

California, San Diego, USA

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Overall Acceptance Rate 129 of 190 submissions, 68%

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Mohácsi MTörök MSáray STar LFarkas GKáli S(2024)Evaluation and comparison of methods for neuronal parameter optimization using the Neuroptimus software frameworkPLOS Computational Biology10.1371/journal.pcbi.101203920:12(e1012039)Online publication date: 23-Dec-2024
https://doi.org/10.1371/journal.pcbi.1012039
Inibhunu HMoradi Chameh HSkinner FRich SValiante T(2023)Hyperpolarization-Activated Cation Channels Shape the Spiking Frequency Preference of Human Cortical Layer 5 Pyramidal Neuronseneuro10.1523/ENEURO.0215-23.202310:8(ENEURO.0215-23.2023)Online publication date: 11-Aug-2023
https://doi.org/10.1523/ENEURO.0215-23.2023
Delorme A(2023)EEG is better left aloneScientific Reports10.1038/s41598-023-27528-013:1Online publication date: 9-Feb-2023
https://doi.org/10.1038/s41598-023-27528-0
Oláh VPedersen NRowan M(2022)Ultrafast simulation of large-scale neocortical microcircuitry with biophysically realistic neuronseLife10.7554/eLife.7953511Online publication date: 7-Nov-2022
https://doi.org/10.7554/eLife.79535
Dorman DBlackwell K(2022)Synaptic Plasticity Is Predicted by Spatiotemporal Firing Rate Patterns and Robust to In Vivo-like VariabilityBiomolecules10.3390/biom1210140212:10(1402)Online publication date: 1-Oct-2022
https://doi.org/10.3390/biom12101402
Moolchand PJones SFrank M(2022)Biophysical and Architectural Mechanisms of Subthalamic Theta under Response ConflictThe Journal of Neuroscience10.1523/JNEUROSCI.2433-19.202242:22(4470-4487)Online publication date: 27-Apr-2022
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Kelley CNewton AHrabetova SMcDougal RLytton W(2022)Multiscale Computer Modeling of Spreading Depolarization in Brain Sliceseneuro10.1523/ENEURO.0082-22.20229:4(ENEURO.0082-22.2022)Online publication date: 4-Aug-2022
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Pham THansel C(2022)Intrinsic threshold plasticity: cholinergic activation and role in the neuronal recognition of incomplete input patternsThe Journal of Physiology10.1113/JP283473601:15(3221-3239)Online publication date: 11-Aug-2022
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Yuan PZhang MTong LMorse TMcDougal RDing HChan DCai YGrutzendler J(2022)PLD3 affects axonal spheroids and network defects in Alzheimer’s diseaseNature10.1038/s41586-022-05491-6612:7939(328-337)Online publication date: 30-Nov-2022
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Bouziane IDas MFriston KCaballero-Gaudes CRay D(2022)Enhanced top-down sensorimotor processing in somatic anxietyTranslational Psychiatry10.1038/s41398-022-02061-212:1Online publication date: 25-Jul-2022
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