From c1bf262982b325ecf2db7c01d1a36f3458fdbefe Mon Sep 17 00:00:00 2001 From: shimoura <renanshimoura@gmail.com> Date: Tue, 15 Aug 2023 15:31:29 +0200 Subject: [PATCH] description of some parameters added --- multi-area-model.ipynb | 29 ++++++++++++++++++----------- 1 file changed, 18 insertions(+), 11 deletions(-) diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb index 146d3ba..392d763 100644 --- a/multi-area-model.ipynb +++ b/multi-area-model.ipynb @@ -197,13 +197,20 @@ "source": [ "| Parameter | Parameter description | Variable | Value | Value description |\n", "|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|\n", - "| | | replace_non_simulated_areas | 'het_poisson_stat' | |\n", - "| | | g | -11. | |\n", - "| | | K_stable | 'K_stable.npy' | |\n", - "| | | fac_nu_ext_TH | 1.2 | |\n", - "| | | fac_nu_ext_5E | 1.125 | |\n", - "| | | fac_nu_ext_6E | 1.41666667 | |\n", - "| | | av_indegree_V1 | 3950. | |" + "| |It defines how non-simulated areas will be replaced | replace_non_simulated_areas | 'het_poisson_stat' |$^1$|\n", + "| |It sets the relative inhibitory synaptic strength | g | -11. |$^2$|\n", + "| |Stabilization method of Schuecker, Schmidt et al. (2017) | K_stable | 'K_stable.npy' |$^3$|\n", + "| |Increase the external input to 2/3E and 5E in area TH | fac_nu_ext_TH | 1. | |\n", + "| |Increase the external Poisson indegree onto 5E | fac_nu_ext_5E | 1.125 | |\n", + "| |Increase the external Poisson indegree onto 6E | fac_nu_ext_6E | 1.41666667 | |\n", + "| |Adjust the average indegree in V1 based on monkey data | av_indegree_V1 | 3950. | |\n", + "| |Scaling factor for cortico-cortical connections (chi) |cc_weights_factor | 1. |$^4$|\n", + "\n", + "Notes: \n", + "1. Whether to replace non-simulated areas by Poisson sources with the same global rate rate_ext ('hom_poisson_stat') or by specific rates ('het_poisson_stat') or by time-varying specific current ('het_current_nonstat'). In the two latter cases, the data to replace the cortico-cortical input is loaded from `replace_cc_input_source`\n", + "2. `g` controls the excitation to inhibition balance in network's activity.\n", + "3. Whether to apply the stabilization method of Schuecker, Schmidt et al. (2017). Default is None. Options are True to perform the stabilization or a string that specifies the name of a binary numpy file containing the connectivity matrix.\n", + "4. This scaling factor controls the cortico-cortical synaptic strength. If it is 1.0 then the inter-area synaptic strength is the same as the intra-areal. This factor changes the network activity from ground to metastable." ] }, { @@ -221,7 +228,7 @@ "source": [ "| Parameter | Parameter description | Variable | Value | Value description |\n", "|:---------:|:----------------------|:-----------------------------:|:--------------------:|:------------------|\n", - "| | | rate_ext | 10. | |" + "| |It defines the rate of the Poissonian spike generator (in spikes/s)| rate_ext | 10. | |" ] }, { @@ -239,8 +246,8 @@ "source": [ "| Parameter | Parameter description | Variable | Value | Value description |\n", "|:---------:|:----------------------|:---------------------------:|:------------------:|:------------------|\n", - "| | | V0_mean | -150. | |\n", - "| | | V0_sd | 50. | |" + "| |Mean for the distribution of initial membrane potentials| V0_mean | -150. | |\n", + "| |Standard deviation for the distribution of initial membrane potentials| V0_sd | 50. | |" ] }, { @@ -323,7 +330,7 @@ "id": "a0730f70-ed9b-4664-b677-3dda965a01ef", "metadata": {}, "source": [ - "### 3. Simulation paramters (sim_params) <a class=\"anchor\" id=\"section_4.3\"></a>\n", + "### 3. Simulation parameters (sim_params) <a class=\"anchor\" id=\"section_4.3\"></a>\n", "Simulation parameters define the paramters that influence the process of simulation, inlcuding the simulation time, the number of processes and theads used to run the simulation.<br>" ] }, -- GitLab