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README.html
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<html>
<p>NEST patch and python files for the model:
<a href="">
A. Marascoa, C. Tribuzi, C. A. Lupascu and M. Migliore. Modeling realistic synaptic inputs of CA1 hippocampal
pyramidal neurons and interneurons via Adaptive Generalized Leaky Integrate-and-Fire models.</a>
</p>
<p>In this study we propose an Adaptive GLIF (A-GLIF) approach that can reproduce experimental findings under variable currents by
incorporating a new set of update rules. The extended A-GLIF model successfully reproduces
both constant and variable current inputs, and it was validated against the results obtained
using a biophysical accurate model neuron. This enhancement provides researchers with a tool
to optimize spiking neuron models using classic experimental traces under constant current
injections, reliably predicting responses to synaptic inputs, which can be confidently used for
large-scale network implementations.
</p>
<p>In order to reproduce Fig. 8 of the paper run first<br/>
python AGLIF_synaptic.py<br/>
in order to get the following files<br/>
6_065_voltage_simulated.txt<br/>
6_065_t_spk_simulated.txt<br/>
and then run<br/>
python figure8.py<br/>
</p>
<p>
The script will produce the following image<br/>
<img src="figure8_2.png" alt="Figure 8">
</p>
<p>Under Ubuntu unix systems:<br/>
install cmake and build-essential:<br/>
sudo apt install cmake<br/>
sudo apt-get install build-essential<br/>
install anaconda3 following instructions from:<br/>
...<br/>
<p>
</p>Create a Conda Enviroment following instructions at https://github.com/nest/nest-simulator/blob/master/environment.yml
OR<br/>
create a conda environment:<br/>
conda create -n nest python=3.9<br/>
conda activate nest<br/>
<br/>
install the following packages:<br/>
conda install -c anaconda numpy<br/>
conda install -c forge matplotlib<br/>
conda install -c conda-forge openmpi<br/>
conda install -c anaconda gsl<br/>
conda install -c anaconda cython<br/>
<br/>
to compile the NEST simulator with our AGLIF model:<br/>
download the correct nest version using:<br/>
git clone https://github.com/nest/nest-simulator.git<br/>
git fetch<br/>
git checkout 01f6e5a763906a3b7cf6713b887366af7bc20a44<br/>
<br/>
Apply the patch:<br/>
git apply patch_ModelDB_synaptic_paper.patch<br/>
<br/>
mkdir ../nest-build<br/>
cd ../nest-build<br/>
cmake ../nest-simulator<br/>
make<br/>
make install<br/>
<br/>
To run the simulation put these files in a new directory:<br/>
membranepot_trace_l23-06-13.res.6-tt6clu2_0.65+1_prova06122022.txt<br/>
run_mds_nest.py<br/>
AGLIF_synaptic_model_MARASCO_et_al.py<br/>
and run:<br/>
conda activate nest<br/>
python AGLIF_synaptic_model_MARASCO_et_al<br/>
new files will be generated:<br/>
spikes.txt<br/>
membranepot_trace_l23-06-13.res.6-tt6clu2_0.65+1_prova06122022.txt<br/>
Model_traces_for_constant_current_injections_NEST.png<br/>
that can be compared with the files generated by us with the same filenames found in the compressed file:<br/>
marasco_etal.zip<br/>
</p>
<p>Questions on how to use this model<br/>
should be directed to michele.migliore at cnr.it<br/>
Questions on how to modifiy or run this<br/>
model should be addressed to smgsolinas at uniss.it<br/>
</p>
<hr>
<p>
Curator's Note (2024-05-05):<br>
<br>
Depending on where you downloaded this from, you may find two zip files
in the <code>marasco_etal</code> folder and one at the top level.
If so, these should be expanded before running the code.
</p>
</body>
</html>