Author: Oscar Javier Avella Gonzalez (oscarjavella at gmail.com) The model was implemented using the Simulation Environment NEURON version 6.0 and uses Matlab V.2009b to analyze the data. All routines are based on general functions of this platform. Paper: Avella Gonzalez, O. J., Van Aerde, K. I., Van Elburg, R. A. J., Poil, S-S., Mansvelder, H. D., Linkenkaer-Hansen, K., Van Pelt, J., and Van Ooyen, A. (2012). External drive to inhibitory cells induces alternating episodes of high- and low-amplitude oscillations. PloS Computational Biology 8(8): e1002666. doi:10.1371/journal.pcbi.1002666 The model and the corresponding set of routines are released under the GNU GPL version 3: http://www.gnu.org/copyleft/gpl.html Purpose of the study: The model was designed to reproduce cortical oscillations, especially those occurring in the beta and gamma band of the frequency spectrum, as observed in the prefrontal cortex (PFC) and hippocampus of rats and humans. Once those oscillation patterns were identified in the model,we focused on the commonly observed but still unexplained fluctuations in oscillation amplitude. We characterized these fluctuations by the durations of high- and low-amplitude episodes (HAE, LAE) of the oscillation. Next, we looked for the particular conditions of the external inputs, i.e. constant depolarizing currents (CDCs) and action potential trains (APs), that were able to generate alternating episodes of high- and low-amplitude oscillations. For further details, see the paper above. Model description: The model consisted of a network of 80 excitatory (E) cells and 20 inhibitory (I) cells, connected with AMPA (excitatory) and GABAa (inhibitory) synapses. The synaptic strength and connection probability was chosen so as to produce a strong PING-like (pyramidal-interneuron gamma) rhythm. Neurons were modeled as: Single compartments. Conductance-based cells with K+, Na+ and leak channels. At the synaptic level: Inhibitory cells project GABAA synapses. Excitatory cells project AMPA synapses. Running the simulation: The model was originally ran on NEURON 6.0 using the conventional commands line scheme, edited in pspad, but any other text editor also works. To set up the simulation example, either auto-launch from ModelDB (in which case the model will automatically run a very short demo of 400ms without writting any files) or download and extract the archive, compile the mod files in the folders mods/other_mods mods/synapse (mknrndll on mswin or mac or nrnivmodl in unix/linux) go to /main directory and load the file "Control_execute_network_bgk.hoc" Once the windows are open, press the button "single run" in the MultipleRuncontrol panel. The simulation will start, running for 40000ms. When the simulation stops, expand the window "Pyram Cells Population # 0" in the horizontal axis, to check for the dynamics of the excitatory population (rastergram). Do the same for the window labeled Fast Spiking Cells Population #0 and check for the inhibitory population dynamics. The results of this "program run" are automatically saved in the file .\output_matlab\WaxingWaning.m Running the example: The example shown in the file .\main\fig3a_b_c.tif can be obtained by double clicking on the filename .\main\run_exampleFig.m into matlab click on "run" and wait for a couple of minutes until the results are displayed: Figure "fig3a_b_c.tif" corresponds to the image of figure 3 of the PloS Comp. Biol. paper above, panels a, b and c. This is a clear example depicting fluctuations in the amplitude of the oscillation, due to the changes in synchrony between the cells, which is high during HAEs and low during LAEs. From top to bottom, the figure shows (a) the rastergram of the excitatory cells, (b) the firing rate histogram (frh) and the corresponding interpolated spline envelope. Finally in the bottom panel, we plotted (c) the wavelet transform of the frh, showing clear fluctuations in the power (amplitude) of the oscillation, for a frequency around 18Hz. Producing the example figure: Open the /main folder and double click on the file "runExampleFigs.m" Once Matlab has loaded it, press the button "run". Manipulating and Changing parameters: To change connection probabilities, synaptic strength, and characteristics of the inputs such as interspike intervals and CDC (current) amplitudes, edit the file \main\functions_net_bgk_multitest_sparse.hoc and check for the respective parameter in lines 7-33 in the file. To change the output file, open the folder \main\sessions and load the file "DrivePower_run_mono_no_spk.ses" and modify the content of line 41 file_name="./output_matlab/WaxingWaning" with the modified name.