From 9957d4cf946c395929dcfd4266d34ceab9862289 Mon Sep 17 00:00:00 2001
From: Didi Hou <d.hou@outlook.com>
Date: Tue, 22 Aug 2023 05:01:55 +0200
Subject: [PATCH] update multi-area-model.ipynb
---
multi-area-model.ipynb | 29 +++++++++++++++++++++--------
1 file changed, 21 insertions(+), 8 deletions(-)
diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index b40d3f3..96a61e2 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -182,8 +182,12 @@
"metadata": {},
"outputs": [],
"source": [
+ "# Model parameters\n",
+ "# Model paramters are most important among all the paramters, it directly affect the model itself and thus have a great impact on the simulation results. Model paramters define the connection, input, neuron, and network charateristics of the model, and therefore fall into four categories: **Connection paramters**, **Input paramters**, **Neuron paramters**, and **Network paramters**.\n",
"scale_down_to = 0.005 # Change it to 1. for running the fullscale network\n",
- "cc_weights_factor = \n",
+ "# Scaling factor for cortico-cortical connections (chi) \n",
+ "# 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.\n",
+ "cc_weights_factor = 1.\n",
"replace_non_simulated_areas = 'het_poisson_stat'\n",
"sim_areas = "
]
@@ -206,13 +210,22 @@
"outputs": [],
"source": [
"# Connection parameters (conn_params)\n",
- "conn_params = {'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.}\n",
+ "conn_params = {\n",
+ " # # It defines how non-simulated areas will be replaced\n",
+ " # 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",
+ " 'replace_non_simulated_areas': 'het_poisson_stat', \n",
+ "\n",
+ " 'g': -11.,\n",
+ " 'K_stable': 'K_stable.npy',\n",
+ " # Increase the external input to 2/3E and 5E in area TH\n",
+ " 'fac_nu_ext_TH': 1.2,\n",
+ " # Increase the external Poisson indegree onto 5E\n",
+ " 'fac_nu_ext_5E': 1.125,\n",
+ " # Increase the external Poisson indegree onto 6E\n",
+ " 'fac_nu_ext_6E': 1.41666667,\n",
+ " # Adjust the average indegree in V1 based on monkey data\n",
+ " 'av_indegree_V1': 3950.\n",
+ "}\n",
"\n",
"# Input parameters (input_params)\n",
"input_params = {'rate_ext': 10.}\n",
--
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