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bulbnet-reproduction

Code associated with the article "[Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model"

https://github.com/apdavison/bulbnet-reproduction

Science Score: 26.0%

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    Low similarity (6.2%) to scientific vocabulary

Keywords

computational-neuroscience neuron-simulator olfaction reproducible-paper rescience simulation
Last synced: 4 months ago · JSON representation

Repository

Code associated with the article "[Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model"

Basic Info
  • Host: GitHub
  • Owner: apdavison
  • License: mit
  • Language: TeX
  • Default Branch: master
  • Size: 13.2 MB
Statistics
  • Stars: 0
  • Watchers: 2
  • Forks: 1
  • Open Issues: 0
  • Releases: 1
Topics
computational-neuroscience neuron-simulator olfaction reproducible-paper rescience simulation
Created over 5 years ago · Last pushed over 5 years ago
Metadata Files
Readme License Authors Codemeta

README.md

bulbnet-reproduction

This is a model of the mammalian olfactory bulb for the NEURON simulator. The model contains only mitral and granule cells.

A full description may be found in: Davison A.P., Feng J. and Brown D. (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. J. Neurophysiol. 90:1921-35

To reproduce the figures from this paper, install NEURON, change to the code directory, run:

$ nrnivmodl

then for each figure run:

$ python run.py figure_2

and similarly for the other figures.

Time required to run simulations

The following times are for running with 32 threads on a workstation with dual Intel Xeon E5-2640 processors (8 cores, 2.6 GHz, 20 MB cache), 128 GB 2400 MHz DDR4 ECC RAM, writing to a 400 GB SSD SAS 12 Gbit/s hard disk. The time to run with a single core was about 10 times as long.

figure_2 1m 19s figure_3 9m 10s figure_4 3m 46s figure_5 3m 56s figure_7 2m 32s figure_8 5m 25s figure_9 14m 58s figure_10 1h 46m figure_11 15m 50s figure_12 10m 42s figure_13 1h 24m figure_14 34m 19s figure_15 8m 46s figure_16 25m 32s figure_17 6m 23s

Dependencies

  • NEURON (https://neuron.yale.edu/neuron/)
  • Gnuplot (http://www.gnuplot.info/)
  • Python (v3.6 or more recent)
  • NumPy
  • PyYAML
  • Jinja2
  • epstopdf (optional - for converting figure to PDF)
  • ImageMagick (optional - for converting figures to PNG)

For more information, contact andrew.davison@cnrs.fr

Owner

  • Name: Andrew Davison
  • Login: apdavison
  • Kind: user
  • Location: France

CodeMeta (codemeta.json) 

{
  "@context": "https://doi.org/10.5063/schema/codemeta-2.0",
  "@type": "SoftwareSourceCode",
  "license": "https://spdx.org/licenses/MIT",
  "codeRepository": "https://github.com/apdavison/bulbnet-reproduction",
  "issueTracker": "https://github.com/apdavison/bulbnet-reproduction/issues",
  "name": "bulbnet-reproduction",
  "description": "This is a model of the mammalian olfactory bulb for the NEURON simulator. The model contains only mitral and granule cells.\n\nA full description may be found in: Davison A.P., Feng J. and Brown D. (2003) Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model. J. Neurophysiol. 90:1921-35 http://doi.org/10.1152/jn.00623.2002",
  "applicationCategory": "neuroscience",
  "developmentStatus": "active",
  "referencePublication": "https://doi.org/10.5281/zenodo.3972130",
  "funder": [
    {
      "@type": "Organization",
      "name": "BBSRC"
    },
    {
      "@type": "Organization",
      "name": "CNRS"
    }
  ],
  "keywords": [
    "olfactory bulb",
    "simulation"
  ],
  "programmingLanguage": [
    "Python",
    "Hoc",
    "NMODL"
  ],
  "relatedLink": [
    "https://senselab.med.yale.edu/modeldb/ShowModel?model=2730"
  ],
  "author": [
    {
      "@type": "Person",
      "@id": "http://orcid.org/0000-0002-4793-7541",
      "givenName": "Andrew",
      "familyName": "Davison",
      "email": "andrew.davison@cnrs.fr",
      "affiliation": {
        "@type": "Organization",
        "name": "Institut des Neurosciences Paris-Saclay, CNRS/Université Paris-Saclay"
      }
    }
  ]
}

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