Literature DB >> 26523124

Early experiences in developing and managing the neuroscience gateway.

Subhashini Sivagnanam1, Amit Majumdar1, Kenneth Yoshimoto1, Vadim Astakhov1, Anita Bandrowski1, MaryAnn Martone1, Nicholas T Carnevale2.   

Abstract

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 this research field, are also implemented for parallel computers and suitable for high performance computing machines. But using these tools on complex high performance computing machines remains a challenge because of issues with acquiring computer time on these machines located at national supercomputer centers, dealing with complex user interface of these machines, dealing with data management and retrieval. The Neuroscience Gateway is being developed to alleviate and/or hide these barriers to entry for computational neuroscientists. It hides or eliminates, from the point of view of the users, all the administrative and technical barriers and makes parallel neuronal simulation tools easily available and accessible on complex high performance computing machines. It handles the running of jobs and data management and retrieval. This paper shares the early experiences in bringing up this gateway and describes the software architecture it is based on, how it is implemented, and how users can use this for computational neuroscience research using high performance computing at the back end. We also look at parallel scaling of some publicly available neuronal models and analyze the recent usage data of the neuroscience gateway.

Entities:  

Keywords:  NEURON; computational neuroscience; high performance computing; science gateway

Year:  2015        PMID: 26523124      PMCID: PMC4624199          DOI: 10.1002/cpe.3283

Source DB:  PubMed          Journal:  Concurr Comput        ISSN: 1532-0626            Impact factor:   1.536


  7 in total

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Journal:  Nat Rev Neurosci       Date:  2006-02       Impact factor: 34.870

2.  Parallel network simulations with NEURON.

Authors:  M Migliore; C Cannia; W W Lytton; Henry Markram; M L Hines
Journal:  J Comput Neurosci       Date:  2006-05-26       Impact factor: 1.621

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Authors:  M L Hines; N T Carnevale
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4.  A virtual imaging platform for multi-modality medical image simulation.

Authors:  Tristan Glatard; Carole Lartizien; Bernard Gibaud; Rafael Ferreira da Silva; Germain Forestier; Frédéric Cervenansky; Martino Alessandrini; Hugues Benoit-Cattin; Olivier Bernard; Sorina Camarasu-Pop; Nadia Cerezo; Patrick Clarysse; Alban Gaignard; Patrick Hugonnard; Hervé Liebgott; Simon Marache; Adrien Marion; Johan Montagnat; Joachim Tabary; Denis Friboulet
Journal:  IEEE Trans Med Imaging       Date:  2013-01       Impact factor: 10.048

Review 5.  Virtual imaging laboratories for marker discovery in neurodegenerative diseases.

Authors:  Giovanni B Frisoni; Alberto Redolfi; David Manset; Marc-Étienne Rousseau; Arthur Toga; Alan C Evans
Journal:  Nat Rev Neurol       Date:  2011-07-05       Impact factor: 42.937

6.  Optimization of Applications with Non-blocking Neighborhood Collectives via Multisends on the Blue Gene/P Supercomputer.

Authors:  Sameer Kumar; Philip Heidelberger; Dong Chen; Michael Hines
Journal:  IPDPS       Date:  2010-04-19

7.  Neuroimaging study designs, computational analyses and data provenance using the LONI pipeline.

Authors:  Ivo Dinov; Kamen Lozev; Petros Petrosyan; Zhizhong Liu; Paul Eggert; Jonathan Pierce; Alen Zamanyan; Shruthi Chakrapani; John Van Horn; D Stott Parker; Rico Magsipoc; Kelvin Leung; Boris Gutman; Roger Woods; Arthur Toga
Journal:  PLoS One       Date:  2010-09-28       Impact factor: 3.240

  7 in total
  7 in total

1.  Functional specification of CCK+ interneurons by alternative isoforms of Kv4.3 auxiliary subunits.

Authors:  Viktor János Oláh; David Lukacsovich; Jochen Winterer; Antónia Arszovszki; Andrea Lőrincz; Zoltan Nusser; Csaba Földy; János Szabadics
Journal:  Elife       Date:  2020-06-03       Impact factor: 8.140

2.  Simulation Neurotechnologies for Advancing Brain Research: Parallelizing Large Networks in NEURON.

Authors:  William W Lytton; Alexandra H Seidenstein; Salvador Dura-Bernal; Robert A McDougal; Felix Schürmann; Michael L Hines
Journal:  Neural Comput       Date:  2016-08-24       Impact factor: 2.026

3.  Integrating unsupervised and reinforcement learning in human categorical perception: A computational model.

Authors:  Giovanni Granato; Emilio Cartoni; Federico Da Rold; Andrea Mattera; Gianluca Baldassarre
Journal:  PLoS One       Date:  2022-05-10       Impact factor: 3.752

4.  Automating NEURON Simulation Deployment in Cloud Resources.

Authors:  David B Stockton; Fidel Santamaria
Journal:  Neuroinformatics       Date:  2017-01

5.  The open EEGLAB portal Interface: High-Performance computing with EEGLAB.

Authors:  Ramón Martínez-Cancino; Arnaud Delorme; Dung Truong; Fiorenzo Artoni; Kenneth Kreutz-Delgado; Subhashini Sivagnanam; Kenneth Yoshimoto; Amitava Majumdar; Scott Makeig
Journal:  Neuroimage       Date:  2020-04-11       Impact factor: 6.556

6.  Enhanced top-down sensorimotor processing in somatic anxiety.

Authors:  Ismail Bouziane; Moumita Das; Karl J Friston; Cesar Caballero-Gaudes; Dipanjan Ray
Journal:  Transl Psychiatry       Date:  2022-07-25       Impact factor: 7.989

7.  A single Markov-type kinetic model accounting for the macroscopic currents of all human voltage-gated sodium channel isoforms.

Authors:  Pietro Balbi; Paolo Massobrio; Jeanette Hellgren Kotaleski
Journal:  PLoS Comput Biol       Date:  2017-09-01       Impact factor: 4.475

  7 in total

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