https://github.com/apdavison/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
computational-neuroscience neuron-simulator olfaction reproducible-paper rescience simulation
Last synced: 5 months ago
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Code associated with the article "[Rp] Dendrodendritic inhibition and simulated odor responses in a detailed olfactory bulb network model"
- Host: GitHub
- URL: https://github.com/apdavison/bulbnet-reproduction
- Owner: apdavison
- License: mit
- Created: 2020-04-29T12:33:12.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2020-08-07T15:33:00.000Z (almost 6 years ago)
- Last Synced: 2025-09-04T18:56:04.905Z (9 months ago)
- Topics: computational-neuroscience, neuron-simulator, olfaction, reproducible-paper, rescience, simulation
- Language: TeX
- Size: 13.2 MB
- Stars: 0
- Watchers: 2
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
- License: LICENSE
- Authors: AUTHORS
- Codemeta: codemeta.json
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README
# 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