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Data Exporter: A complementary tool to export data simulation from NEURON.

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Title: Data Exporter: A complementary tool to export data simulation from NEURON.
Alternate Title: Data Exporter: Una herramienta complementaria para exportar datos obtenidos de simulaciones con NEURON.
Authors: Hernández, Óscar Emilio1 ohernandezb@uninorte.edu.co, Jabba, Daladier2, Muñoz, Fabián3
Source: Salud Uninorte. 2013, Vol. 29 Issue 2, p288-297. 10p.
Subjects: COMPUTER simulation, BIOPHYSICAL labeling, COMPUTATIONAL neuroscience, MATLAB (Computer software), NEURONS, ACTION potentials
Abstract (English): Objectives: To develop a computational tool for NEURON simulation environment, user friendly, to store the results generated during simulation and to make subsequent analysis with other tools such as Matlab and IgorPRo. Materials and Methods: Data Exporter was implemented in the programming language hoc. This algorithm is divided in 13 sections or blocks. The first section is necessary to edit in a new simulation. These new configuration determine the geometry, biophysic properties the neurons to simulate and path to save data. Results: To check the efficiency of the algorithm, we simulated the propagation of action potential in TRN(thalamic reticular nucleus) neuron in different large of simulation. We determine that the time of simulation is linear respect to time of simulation. Conclusions: Data Exporter makes easier to start to neural simulation in NEURON reducing the steps of programming to geometry and biophysical properties of the neuron and to allow save data to next steps of analysis. [ABSTRACT FROM AUTHOR]
Abstract (Spanish): Objetivos: Desarrollar una herramienta computacional en ambiente lenguaje de programación hoc de NEURON y de fácil uso, que permita el rápido almacenamiento de los resultados obtenidos para su posterior análisis en otros software tales como Matlab or IgorPro. Materiales y métodos: Para el desarrollo de Data Exporter se escribió un algoritmo en lenguaje de programación hoc de NEURON. El algoritmo, escrito en un único archivo de texto, esta dividido en 13 bloques, de los cuales solo el primero debe ser modificado para adaptarlo a una geometría y biofísica neuronal particular y para determinar la ruta de almacenamiento de los datos. Resultados: Se desarrollo un software que simula la propagación de potenciales de acción a través de geometrías neuronales complejas. El uso de esta herramienta permite el almacenamiento de los resultados obtenidos, como potenciales y corrientes de membrana en diferentes puntos de toda la neurona, sin incremento significativo en el tiempo para el desarrollo de los procesos. Conclusiones: Data Exporter es un software que le da mayor flexibilidad a NEURON facilitando el acceso a nuevos neurocientíficos, los cuales pueden usarlo con solo conocer los códigos necesarios para el desarrollo de los archivos relacionados con las propiedades geométricas y biofísicas neuronales. [ABSTRACT FROM AUTHOR]
Copyright of Salud Uninorte is the property of Fundacion Universidad del Norte and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract. (Copyright applies to all Abstracts.)
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  Data: Data Exporter: A complementary tool to export data simulation from NEURON.
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  Data: Data Exporter: Una herramienta complementaria para exportar datos obtenidos de simulaciones con NEURON.
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  Data: <searchLink fieldCode="AR" term="%22Hernández%2C+Óscar+Emilio%22">Hernández, Óscar Emilio</searchLink><relatesTo>1</relatesTo><i> ohernandezb@uninorte.edu.co</i><br /><searchLink fieldCode="AR" term="%22Jabba%2C+Daladier%22">Jabba, Daladier</searchLink><relatesTo>2</relatesTo><br /><searchLink fieldCode="AR" term="%22Muñoz%2C+Fabián%22">Muñoz, Fabián</searchLink><relatesTo>3</relatesTo>
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  Data: <searchLink fieldCode="JN" term="%22Salud+Uninorte%22">Salud Uninorte</searchLink>. 2013, Vol. 29 Issue 2, p288-297. 10p.
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  Data: <searchLink fieldCode="DE" term="%22COMPUTER+simulation%22">COMPUTER simulation</searchLink><br /><searchLink fieldCode="DE" term="%22BIOPHYSICAL+labeling%22">BIOPHYSICAL labeling</searchLink><br /><searchLink fieldCode="DE" term="%22COMPUTATIONAL+neuroscience%22">COMPUTATIONAL neuroscience</searchLink><br /><searchLink fieldCode="DE" term="%22MATLAB+%28Computer+software%29%22">MATLAB (Computer software)</searchLink><br /><searchLink fieldCode="DE" term="%22NEURONS%22">NEURONS</searchLink><br /><searchLink fieldCode="DE" term="%22ACTION+potentials%22">ACTION potentials</searchLink>
– Name: Abstract
  Label: Abstract (English)
  Group: Ab
  Data: Objectives: To develop a computational tool for NEURON simulation environment, user friendly, to store the results generated during simulation and to make subsequent analysis with other tools such as Matlab and IgorPRo. Materials and Methods: Data Exporter was implemented in the programming language hoc. This algorithm is divided in 13 sections or blocks. The first section is necessary to edit in a new simulation. These new configuration determine the geometry, biophysic properties the neurons to simulate and path to save data. Results: To check the efficiency of the algorithm, we simulated the propagation of action potential in TRN(thalamic reticular nucleus) neuron in different large of simulation. We determine that the time of simulation is linear respect to time of simulation. Conclusions: Data Exporter makes easier to start to neural simulation in NEURON reducing the steps of programming to geometry and biophysical properties of the neuron and to allow save data to next steps of analysis. [ABSTRACT FROM AUTHOR]
– Name: Abstract
  Label: Abstract (Spanish)
  Group: Ab
  Data: Objetivos: Desarrollar una herramienta computacional en ambiente lenguaje de programación hoc de NEURON y de fácil uso, que permita el rápido almacenamiento de los resultados obtenidos para su posterior análisis en otros software tales como Matlab or IgorPro. Materiales y métodos: Para el desarrollo de Data Exporter se escribió un algoritmo en lenguaje de programación hoc de NEURON. El algoritmo, escrito en un único archivo de texto, esta dividido en 13 bloques, de los cuales solo el primero debe ser modificado para adaptarlo a una geometría y biofísica neuronal particular y para determinar la ruta de almacenamiento de los datos. Resultados: Se desarrollo un software que simula la propagación de potenciales de acción a través de geometrías neuronales complejas. El uso de esta herramienta permite el almacenamiento de los resultados obtenidos, como potenciales y corrientes de membrana en diferentes puntos de toda la neurona, sin incremento significativo en el tiempo para el desarrollo de los procesos. Conclusiones: Data Exporter es un software que le da mayor flexibilidad a NEURON facilitando el acceso a nuevos neurocientíficos, los cuales pueden usarlo con solo conocer los códigos necesarios para el desarrollo de los archivos relacionados con las propiedades geométricas y biofísicas neuronales. [ABSTRACT FROM AUTHOR]
– Name: AbstractSuppliedCopyright
  Label:
  Group: Ab
  Data: <i>Copyright of Salud Uninorte is the property of Fundacion Universidad del Norte and its content may not be copied or emailed to multiple sites without the copyright holder's express written permission. Additionally, content may not be used with any artificial intelligence tools or machine learning technologies. However, users may print, download, or email articles for individual use. This abstract may be abridged. No warranty is given about the accuracy of the copy. Users should refer to the original published version of the material for the full abstract.</i> (Copyright applies to all Abstracts.)
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      – Code: eng
        Text: English
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      Pagination:
        PageCount: 10
        StartPage: 288
    Subjects:
      – SubjectFull: COMPUTER simulation
        Type: general
      – SubjectFull: BIOPHYSICAL labeling
        Type: general
      – SubjectFull: COMPUTATIONAL neuroscience
        Type: general
      – SubjectFull: MATLAB (Computer software)
        Type: general
      – SubjectFull: NEURONS
        Type: general
      – SubjectFull: ACTION potentials
        Type: general
    Titles:
      – TitleFull: Data Exporter: A complementary tool to export data simulation from NEURON.
        Type: main
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    HasContributorRelationships:
      – PersonEntity:
          Name:
            NameFull: Hernández, Óscar Emilio
      – PersonEntity:
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            NameFull: Jabba, Daladier
      – PersonEntity:
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            NameFull: Muñoz, Fabián
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            – D: 01
              M: 05
              Text: 2013
              Type: published
              Y: 2013
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              Value: 29
            – Type: issue
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          Titles:
            – TitleFull: Salud Uninorte
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