## This a NEURON + Python2 script associated with the paper:

Ruben A. Tikidji-Hamburyan, Carmen C. Canavier

**Shunting Inhibition Improves Synchronization in Heterogeneous Inhibitory Interneuronal Networks with Type 1 Excitability Whereas Hyperpolarizing Inhibition is Better for Type 2 Excitability **

*eNeuro (in press)*

## Requirements

To use this scripts you need **Python 2.7** and python's libraries:

- numpy
- scipy
- matplotlib and LaTeX for correct graphical interface

Under Ubuntu or any other Debian based Linux, run *sudo apt-get install python-numpy python-scipy python-matplotlib texlive-full*. 

You can use *yum* or *zymm* under RadHad or SUSE based Linux distributions.

## Examples from the paper
To run simulations:

- nrnivmodl
- nrngui -nogui -python network.py **[parameters]**

**[paramters]** for different figures are given below

### Figure 3A
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /tv=0,1000 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Istdev=1.5e-2 /neuron/Vinit=-50.,20 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=5e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-75.0
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/nrnFRhist/range=-0.05,0.85 /nrnFRhist/bins=9 
/nrnFRhist/xnorm=True /nrnFRhist/ymax=0.5 /sortbysk=FR /nrnISI=100 /nrnFRhist/part=True 
`

### Figure 3B
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /tv=0,1000 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Istdev=1.5e-2 /neuron/Vinit=-50.,20. /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=5e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-75.0
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/nrnFRhist/range=-0.05,0.85 /nrnFRhist/bins=9 
/nrnFRhist/xnorm=True /nrnFRhist/ymax=0.5 /sortbysk=FR /nrnISI=100 /nrnFRhist/part=True 
`

### Figure 3C [$^2$](#note2)
`
nrngui -nogui -python network.py /git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Vinit=-51.0,20.0  /neuron/Istdev=YYYY\*1e-2 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=XXX\*1e-2 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-75.0 
/tstop=2500 /cliptrn=500
`

where XXX is a synaptic conductance and YYYY is a level of noise. The scale 1e-2 converts nA into uA/cm2 and uS into mS/cm2.
 
### Figure 3D [$^2$](#note2)
`
nrngui -nogui -python network.py /git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Vinit=-51.0,20.0  /neuron/Istdev=YYYY*1e-2 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=XXX*1e-2 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-75.0 
/tstop=2500 /cliptrn=500
`

where XXX is a synaptic conductance and YYYY is a level of noise.

### Figure 4A and supplementary movie sp1-20190619163238.mp4 [$^1$](#note1)
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /sortbysk=I /tv=400,500 /ncell=300 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Istdev=1.5e-2 /neuron/Vinit=-68 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=5e-4 /synapse/delay=0.7,3.5 /delay-dist="UNIFORM"
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/pop-pp-view=True /PhaseLims=(-76,-20),(0.3,0.6) /pop-pp-view-color=True 
`

### Figure 4B and supplementary movie sp2-20190619165631.mp4 [$^1$](#note1)
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /sortbysk=I /tv=400,500 /ncell=300 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Istdev=1.5e-2 /neuron/Vinit=-68 /neuron/Iapp='u',0.02,0.037 
/synapse/weight=5e-4 /synapse/delay=0.7,3.5 /delay-dist="UNIFORM" 
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/pop-pp-view=True /PhaseLims=(-76,-20),(0.3,0.6)  /pop-pp-view-color=True 
`

### Figure 5A
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /tv=0,1000 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Istdev=1.5e-2 /neuron/Vinit=-50.,20 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=15e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.0
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/nrnFRhist/range=-0.05,0.85 /nrnFRhist/bins=9 
/nrnFRhist/xnorm=True /nrnFRhist/ymax=0.5 /sortbysk=FR /nrnISI=100 /nrnFRhist/part=True 
`

### Figure 5B
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /tv=0,1000 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Istdev=1.5e-2 /neuron/Vinit=-50.,20. /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=15e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.0
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/nrnFRhist/range=-0.05,0.85 /nrnFRhist/bins=9 
/nrnFRhist/xnorm=True /nrnFRhist/ymax=0.5 /sortbysk=FR /nrnISI=100 /nrnFRhist/part=True 
`

### Figure 5C [$^2$](#note2)
`
nrngui -nogui -python network.py /git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Vinit=-51.0,20.0  /neuron/Istdev=YYYY*1e-2 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=XXX*1e-2 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.0 
/tstop=2500 /cliptrn=500
`

where XXX is a synaptic conductance and YYYY is a level of noise.
 
### Figure 5D [$^2$](#note2)
`
nrngui -nogui -python network.py /git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Vinit=-51.0,20.0  /neuron/Istdev=YYYY*1e-2 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=XXX*1e-2 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.0 
/tstop=2500 /cliptrn=500
`

where XXX is a synaptic conductance and YYYY is a level of noise.

### Figure 6A and supplementary movie sp3-20190619103132.mp4 [$^1$](#note1)
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /sortbysk=I /tv=400,500 /ncell=300 /ncon=\'b\',0.133
/neuron/Type=1 /neuron/Istdev=1.5e-2 /neuron/Vinit=-68 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=15e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/pop-pp-view=True /PhaseLims=(-76,-20),(0.3,0.6) /pop-pp-view-color=True 
`

### Figure 6B and supplementary movie sp4-20190619104959.mp4 [$^1$](#note1)
`
nrngui -nogui -python network.py /gui=ON /git=False /preview=ON /sortbysk=I /tv=400,500 /ncell=300 /ncon=\'b\',0.133
/neuron/Type=2 /neuron/Istdev=1.5e-2 /neuron/Vinit=-68 /neuron/Iapp=\'u\',0.02,0.037 
/synapse/weight=15e-4 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/Esyn=-65.
/ttFFT=False /tracetail=p2eLFP /N2NHI=False 
/pop-pp-view=True /PhaseLims=(-76,-20),(0.3,0.6) /pop-pp-view-color=True 
`

### Figure 7 A1
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037 
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM 
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I 
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=5.e-06 /singmod/per=200.0 
`

### Figure 7 A2
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133 
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=5.e-06 /singmod/per=200.0  
`

### Figure 7 B1
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM 
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I 
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=2.e-06 /singmod/per=100.0  
`

### Figure 7 B2
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037 
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133 /corefunc=24
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I 
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=2.e-06 /singmod/per=100.0  
`

### Any point on heatmap Figure 7 C1 [$^2$](#note2)
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037 
/git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM 
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=20000.0 /tstop=20000.0 /singmod/gmax=XXXX*1e-2 /singmod/per=1000./YYYY
`

where XXXX is modulation conductance in $\mu A/cm^2$ and YYYY is modulation frequency in Hz

### Any point on heatmap Figure 7 C2 [$^2$](#note2)
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037 
/git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133
/synapse/weight=0.001 /synapse/Esyn=-75.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM 
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True 
/singmod/E=-75.0 /singmod/tstart=0 /singmod/tstop=20000.0 /tstop=20000.0 /singmod/gmax=XXXX*1e-2 /singmod/per=1000./YYYY
`

where XXXX is modulation conductance in $\mu A/cm^2$ and YYYY is modulation frequency in Hz

### Figure 8 A1
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Iapp=2.85e-2 /neuron/Istdev=3.e-2 /neuron/Vinit=-68
/gui=ON /git=ON /preview=ON /tv=0,500
/synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/weight=1e-3 
/singmod/tstart=-100 /singmod/tstop=methods['tv'][1] /singmod/gmax=2e-6 /singmod/per=200 
/tracetail=p2eLFP /ttFFT=False /p2eLFP_max=250. /sortbysk=T 
`

### Figure 8 A2
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Iapp=2.85e-2 /neuron/Istdev=3.e-2 /neuron/Vinit=-68
/gui=ON /git=ON /preview=ON /tv=0,500
/synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/weight=1e-3 
/singmod/tstart=-100 /singmod/tstop=methods['tv'][1] /singmod/gmax=2e-6 /singmod/per=200 
/tracetail=p2eLFP /ttFFT=False /p2eLFP_max=250. /sortbysk=T 
`


### Figure 8 B1
`
nrngui -nogui -python  network.py
/neuron/Type=1 /neuron/Iapp=2.85e-2 /neuron/Istdev=3.e-2 /neuron/Vinit=-68 
/gui=ON /git=ON /preview=ON /tv=0,500 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/weight=1e-3 
/singmod/tstart=-50 /singmod/tstop=methods['tv'][1] /singmod/gmax=2e-6 /singmod/per=100 
/tracetail=p2eLFP /ttFFT=False /p2eLFP_max=250. /sortbysk=T 
`

### Figure 8 B2
`
nrngui -nogui -python  network.py
/neuron/Type=2 /neuron/Iapp=2.85e-2 /neuron/Istdev=3.e-2 /neuron/Vinit=-68 
/gui=ON /git=ON /preview=ON /tv=0,500 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM /synapse/weight=1e-3 
/singmod/tstart=-50 /singmod/tstop=methods['tv'][1] /singmod/gmax=2e-6 /singmod/per=100 
/tracetail=p2eLFP /ttFFT=False /p2eLFP_max=250. /sortbysk=T 
`

### Figure 9 A 
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133 
/synapse/weight=0.001 /synapse/Esyn=-65.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I
/singmod/E=-65.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=8.e-06 /singmod/per=200.0  
`

### Figure 9 B
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=ON /preview=ON /ncell=300 /ncon=\'b\',0.133 
/synapse/weight=0.001 /synapse/Esyn=-65.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True /sortbysk=I
/singmod/E=-65.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tv=0.,2000.0 /singmod/gmax=8.e-06 /singmod/per=200.0  
`

### Any point on heatmap Figure 9 C1  [$^2$](#note2)
`
nrngui -nogui -python  network.py 
/neuron/Type=1 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133 
/synapse/weight=0.001 /synapse/Esyn=-65.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True 
/singmod/E=-65.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tstop=2000.0 /singmod/gmax=XXXX*1.e-02 /singmod/per=1000./YYYY  
`

where XXXX is modulation conductance in $\mu A/cm^2$ and YYYY is modulation frequency in Hz

### Any point on heatmap Figure 9 C2 [$^2$](#note2)
`
nrngui -nogui -python  network.py 
/neuron/Type=2 /neuron/Vinit=-51.0,20.0 /neuron/Istdev=0.03 /neuron/Iapp=\'u\',0.02,0.037
/git=False /gui=False /preview=False /ncell=300 /ncon=\'b\',0.133 
/synapse/weight=0.001 /synapse/Esyn=-65.0 /synapse/delay=0.7,3.5 /delay-dist=UNIFORM
/tracetail=p2eLFP /p2eLFP_max=250 /ttFFT=False /PAC-VS=True 
/singmod/E=-65.0 /singmod/tstart=0 /singmod/tstop=2000.0 /tstop=2000.0 /singmod/gmax=XXXX*1.e-02 /singmod/per=1000./YYYY  
`

where XXXX is modulation conductance in $\mu A/cm^2$ and YYYY is modulation frequency in Hz

### For Figures 10
Use parameters for Figures 3C, 3D, 5C, 5D, 9C1, or 9C2  as above and add `/neuron/distribution/F=\'n\',1.04,0.4` to the end of command line.

### Notes
1. <a name="note1"></a>For Figures 4A, 4B, 6A, and 6B, if you click on phase-plot window, you can explore evolution of population dynamics using page-up/page-down keys.
2. <a name="note2"></a>Simulations for Figures 3C, 3D, 5C, 5D, 7C, and 9C will not show anything on the screen. All results are saved in the `network.simdb` file. 
`simdb` has a very simple format: each simulation is a line. Column `:` separates recorded fields. Each field is a couple `key=value` with the equal symbol as a separator.
*An example of fields in a simulation record* shows R2-index of network synchronization, spike-per-cycle, and neurons firing rate to network frequency ratio:
`/R2-results/R2=0.80846372802:/R2-results/spc=88.1:/R2-results/stdr_Fr/Fnet=0.264655449759`

## Files in this directory
| File              | Description                                      |
|:------------------|:-------------------------------------------------|
| network.py        | main script                                      |
|norm_translation.py| subroutine for synapses amplitude normalization (wasn't used in the paper) |
|type21v02.mod      | NEURON module for membrane currents of a single neuron|
|innp.mod           | noise current generator, writen by Ted Carnevale |
| sinGstim.mod      | module for sinusoidal conductance modulation     |
| sinIstim.mod      | module for sinusoidal current modulation         (wasn't used in the paper) |
 
## Changelog
2022-05: Updated MOD files to contain valid C++ and be compatible with the upcoming versions 8.2 and 9.0 of NEURON.