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.
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
- 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