nico202 / closedlooproessertetal Goto Github PK

This contains the models, functions and resulting data as used in:

Roessert C, Dean P, Porrill J (2015) At the Edge of Chaos: How Cerebellar Granular Layer Network Dynamics Can Provide the Basis for Temporal Filters. PLoS Comput Biol 11(10): e1004515. doi:10.1371/journal.pcbi.1004515

It is based on code used for Yamazaki T, Tanaka S (2005) Neural modeling of an internal clock. Neural Comput 17:1032-58


1. Recompile if necessary. In ./cells/ifun execute:
python setup.py build_ext --inplace
python setup2.py build_ext --inplace
python setup2b.py build_ext --inplace
python setup2re.py build_ext --inplace

2. To plot the figures from the saved data files execute the commands below.
Figures will be saved to: ./figs/Pub

# FIGURE 2
python Plots_Closedloop.py -o fig1 -nompi

# FIGURE 3:
python Plots_Closedloop.py -o fig2 -nompi

# FIGURE 4:
python Plots_Closedloop.py -o fig3 -nompi

# FIGURE 5:
python Plots_Closedloop.py -o fig3b -nompi

# FIGURE 6:
python Plots_Closedloop.py -o fig4l -nompi

# FIGURE 7:
python Plots_Closedloop.py -o fig51l -nompi

# FIGURE 8:
python Plots_Closedloop.py -o fig52l -nompi

# FIGURE 9:
python Plots_Closedloop.py -o figRe6 -nompi


3. Run the actual simulations:
Data will be saved to ./data
Intermediate figure will be saved to ./figs/dump and ./figs/Pub

- To run a single instance of the one-population network execute:
python Plots_Closedloop.py -o ifun -nompi

- To generate a single trace for e.g. Fig 6 it is better to use a cluster. Here is an example to run it on a cluster using Sun Grid Engine:
qsub -v J=Plots_Closedloop.py,O=fig4lruntest -pe ompigige 64 -l rmem=32G -l mem=32G PBSinsigneo.sh

- Run a trace with recurrent filter (Fig 9):
qsub -v J=Plots_Closedloop.py,O=figRe6runtest -pe ompigige 64 -l rmem=32G -l mem=32G PBSinsigneo.sh


A snapshot of the code can also be found on ModelDB: https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=168950


** Terms of use:

This code, "ClosedLoopRoessertEtAl", is a derivative of "internalclock" by Takeru Honda and Tadashi Yamazaki 
used under CC-BY (http://creativecommons.org/licenses/by/3.0/). 
The code of "internalclock" was downloaded from https://senselab.med.yale.edu/ModelDB/ShowModel.cshtml?model=115966
"ClosedLoopRoessertEtAl" is licensed under CC BY by Christian Rössert (christian.a [4t] roessert.de).