Embedded Files
This model was created in the NetLogo framework based on the paper https://journals.plos.org/ploscompbiol/article?id=10.1371/journal.pcbi.1009239. New parameter values were identified in order to reproduce the experimental resting membrane potential of a piriform cortex neuron (-55mv aprox) at postnatal day 14.
The reversal potential of ions varies over time in response to GABAergic synaptic input. In the manuscript, we demonstrate that varying the concentrations of NKCC and KCC leads to differences in both the number of spikes and the firing rate.”
In this link you will have access to the data (results of simulations 4 groups and control group) : https://drive.google.com/file/d/1UCPDFrJeiK_u30rW4F3dgfCAFo7Mbc9u/view?usp=drive_link
The ZIP file contains all the original Netlogo codes for the groups: https://drive.google.com/file/d/1kbQeM2rkko_ZAp-dKZbe6kwFhl-nD0LV/view?usp=sharing
Each group has a stopping time used to save the data: if ticks = 7000000 [ export-world "groupX" set sina 1] This exports a snapshot of the code state that can be loaded into NetLogo at that tick value, which avoids having to run the simulation again for a long time until reaching the stable version. After that, the simulation can continue for the next stage of the experiment.
We also provide an commented Netlogo code version of the simulation mechanisms in HHion_commented:
https://drive.google.com/file/d/13tEIbjG5qHkWZGuqCmsz3l3Kwv2qF9QG/view?usp=sharing Here, you will be able to run the code online using NetLogo Web
“To run the model online, follow the instructions:
Download HHion_commented.nlogo: https://drive.google.com/file/d/13tEIbjG5qHkWZGuqCmsz3l3Kwv2qF9QG/view?usp=sharing
On the next page, upload the file HHion_commented.nlogo using ‘Upload a Model: Browse’.or https://www.netlogoweb.org/launch#NewModel
Click Create and then Go.”
You can run the model and generate an input using the button. Every 2500 ticks, the plots are reset. You can edit line 444, changing:
if mmm = (2500 - 1) [set s_i sina clear-all-plots] to: if mmm = (2500 - 1) [set s_i sina] This way, you can run the model here in NetLogo Web without resetting the plots.
It is also possible to run the model on your computer. To do so, you need to install NetLogo from NetLogo Home or Download any NetLogo version 6.4.0
The following example, the figure shows the simulation at 2762.8ms. You can see that with 100% activity of KCC and NKCC, the membrane potential remains stable at –55 mV. aprox.
This figure shows the neural activity in response to a GABAergic synaptic input. (This visualization is generated when the model is run on a PC.)
The reversal potential of ions varies over time in response to GABAergic synaptic input. In the manuscript, we demonstrate that varying the concentrations of NKCC and KCC leads to differences in both the number of spikes and the firing rate.”
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