PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
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<!DOCTYPE html PUBLIC "-//W3C//DTD XHTML 1.0 Strict//EN" "http://www.w3.org/TR/xhtml1/DTD/xhtml1-strict.dtd"> <html xmlns="http://www.w3.org/1999/xhtml"> <head> <title></title> <meta name="generator" content="HTML::TextToHTML v2.51"/> </head> <body> <p> <h4> <h3>These NEURON + Python scripts associated with paper:</h3><br/> Ruben A. Tikidji-Hamburyan, Joan Jose Martinez, John A. White, Carmen C. Canavier<br/> Resonant interneurons can increase robustness of gamma oscillations<br/> <i>J Neuroscience 2015 35(47): 15682-15695; doi: 10.1523/JNEUROSCI.2601-15.2015</i><br/> </h4> </p><hr/> <p>To use this scripts you need python libraries: <ol> <li><a ref="http://www.numpy.org">numpy</a></li> <li><a ref="http://www.scipy.org">scipy</a></li> <li><a ref="http://matplotlib.org">matplotlib</a> and LaTeX for correct graphical interface</li> </ol> Under <u>Ubuntu</u> or any other <u>Debian</u> based Linux, run <b>sudo apt-get install python-numpy python-scipy python-matplotlib texlive-full</b>. You can use yum or zymm under RadHad or SUSE based Linux distributions. </p><hr/> <p> To run simulations the network of resonators: <ol> <li><b>cd resonator</b></li> <li><b>nrnivmodl</b></li> <li><b>nrngui -nogui -python network.py --help</b></li> </ol> Last command prints out a short HOWTO and the list of parameters on screen, but does <b>not</b> run simulation. You can use printed parameters to replicate Figures in the paper. </p> <p> For example, to replicate Figure 4 run:<br/> <b>nrngui -nogui -python network.py -Iapp=0.15e-5 -gsyn=3e-7 -nstart='(900.,0.21e-5,1000)' -Istd=0 -gui -view </b><br/> <img src="Figure4.jpg" width="50%" alt="Figure 4" align="center"> </p> <p> or to replicate Figure 9C3 run:<br/> <b>nrngui -nogui -python network.py -Istd=0 -Iapp=0.2e-5 -gsyn=0.005e-5 -delay=1 -view -gui -tstop=5000 -F=1,0.1125 -c=299 -Vinit=-65 -sort=F</b><br/> <img src="Figure9C3.jpg" width="50%" alt="Figure 4" align="center"> </p> <hr/> <p> To run simulations the network of integrators: <ol> <li><b>cd integrator</b></li> <li><b>nrnivmodl</b></li> <li><b>nrngui -nogui -python network.py --help</b></li> </ol> Again last one will print out short HOWTO. </p> <p> For example, to replicate Figure 9C1 run:<br/> <b>nrngui -nogui -python -isatty network.py -Istd=0 -Iapp=0.0005,4.5e-5 -gsyn=1e-7 -delay=1 -view -gui -tstop=5000 -c=299 -Vinit=-65 </b><br/> <img src="Figure9C1.jpg" width="50%" alt="Figure 4" align="center"> </p> <p> and to replicate Figure 9C2 run:<br/> <b>nrngui -nogui -python -isatty network.py -Istd=0 -Iapp=0.0005,4.5e-5 -gsyn=1.25e-5 -delay=1 -view -gui -tstop=5000 -c=299 -Vinit=-65 </b><br/> <img src="Figure9C2.jpg" width="50%" alt="Figure 4" align="center"> </p> </body> </html>
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PIR gamma oscillations in network of resonators (Tikidji-Hamburyan et al. 2015)
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