diff --git a/multi-area-model.ipynb b/multi-area-model.ipynb
index c39ff1cf499f4cb43dbe95b446445ede259b223e..d86c05ad688177b5321f391471b9aa55f5249f68 100644
--- a/multi-area-model.ipynb
+++ b/multi-area-model.ipynb
@@ -234,7 +234,7 @@
"metadata": {},
"source": [
"1. `scale_down_to` <br>\n",
- "scale_down_to is the down-scaling factor which defines the the ratio of the full scale multi-area model being down-scaled to a model with fewer neurons and indegrees so as to be simulated on machines with lower computational ability and the simulation results can be obtained within relative shorter period of time. <br> Its deafualt value if `1.` meaning full scale simulation. <br> In the pre-set downscale version, it's set as `0.005`, where the numer of neurons and indegrees are both scaled down to 0.5% of its full scale amount, where the model can usually be simulated on a local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br> \n",
+ "It is the down-scaling factor that defines the ratio by which the full-scale multi-area model is reduced to a model with fewer neurons and indegrees. This reduction is essential to enable simulation on machines with limited computational power, ensuring that simulation results can be obtained in a relatively shorter timeframe. <br> If the value is `1.`, the full-scale network will be simulated. <br> In the pre-set downscale version, it is set as `0.005`, where the number of neurons and indegrees are scaled down to 0.5% of its full-scale amount, where the model can usually be simulated on a local machine. <br> **Warning**: This will not yield reasonable dynamical results from the network and is only meant to demonstrate the simulation workflow <br> \n",
"2. `cc_weights_factor` <br>\n",
"This scaling factor controls the cortico-cortical synaptic strength. <br> By default it's set as `1.0`, where the inter-area synaptic strength is the same as the intra-areal. <br> **Important**: This factor changes the network activity from ground state to metastable state. <br>\n",
"3. `areas_simulated` <br>\n",
@@ -242,7 +242,7 @@
"complete_area_list = `['V1', 'V2', 'VP', 'V3', 'V3A', 'MT', 'V4t', 'V4', 'VOT', 'MSTd', 'PIP', 'PO', 'DP', 'MIP', 'MDP', 'VIP', 'LIP', 'PITv', 'PITd', 'MSTl', 'CITv', 'CITd', 'FEF', 'TF', 'AITv', 'FST', '7a', 'STPp', 'STPa', '46', 'AITd', 'TH']` <br>\n",
"The value assigned to simulation_areas can be any sublist of the compete_area_list specifying areas a user want to include in his/her simulation. <br>\n",
"4. `replace_non_simulated_areas` <br>\n",
- "The paramter replace_non_simulated_areas defines how non-simulated areas will be replaced. <br> It's set as `None` by default when the parameter areas_simulated is set as full_area_list where all areas will be simulated so that no areas need to be replaced. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`. `'hom_poisson_stat'` is a manually set parameter which can be tuned. When it's set as 'het_poisson_stat' or 'het_current_nonstat', the data to replace the cortico-cortical input is loaded from 'replace_cc_input_source' which is the firing rates of our full scale simulation results. The differenc between 'het_poisson_stat' and 'het_current_nonstat' is that 'het_poisson_stat' is the mean of the time-series firing rate so that it's static, yet 'het_current_nonstat' is time-varying specific current, which is varying by time. "
+ "This parameter defines how non-simulated areas will be replaced. <br> It is set as `None` by default when the parameter areas_simulated is set as full_area_list where all areas will be simulated so that no areas need to be replaced. <br> Other options are: `'hom_poisson_stat'`, `'het_poisson_stat'`, and `'het_current_nonstat'`. `'hom_poisson_stat'` is a manually set parameter which can be tuned. When it is set as 'het_poisson_stat' or 'het_current_nonstat', the data to replace the cortico-cortical input is loaded from 'replace_cc_input_source' which is the firing rates of our full scale simulation results. The differenc between 'het_poisson_stat' and 'het_current_nonstat' is that 'het_poisson_stat' is the mean of the time-series firing rate so that it is static, yet 'het_current_nonstat' is time-varying specific current, which is varying by time. "
]
},
{
@@ -496,7 +496,7 @@
"output_type": "stream",
"text": [
"Initializing network from dictionary.\n",
- "RAND_DATA_LABEL 939\n"
+ "RAND_DATA_LABEL 2177\n"
]
},
{
@@ -576,74 +576,74 @@
"name": "stdout",
"output_type": "stream",
"text": [
- "Prepared simulation in 0.00 seconds.\n",
+ "Prepared simulation in 0.01 seconds.\n",
"Rank 0: created area V1 with 0 local nodes\n",
- "Memory after V1 : 1515.89 MB\n",
+ "Memory after V1 : 1514.66 MB\n",
"Rank 0: created area V2 with 0 local nodes\n",
- "Memory after V2 : 1542.60 MB\n",
+ "Memory after V2 : 1541.36 MB\n",
"Rank 0: created area VP with 0 local nodes\n",
- "Memory after VP : 1571.77 MB\n",
+ "Memory after VP : 1570.57 MB\n",
"Rank 0: created area V3 with 0 local nodes\n",
- "Memory after V3 : 1600.05 MB\n",
+ "Memory after V3 : 1598.81 MB\n",
"Rank 0: created area V3A with 0 local nodes\n",
- "Memory after V3A : 1620.03 MB\n",
+ "Memory after V3A : 1618.78 MB\n",
"Rank 0: created area MT with 0 local nodes\n",
- "Memory after MT : 1645.53 MB\n",
+ "Memory after MT : 1644.28 MB\n",
"Rank 0: created area V4t with 0 local nodes\n",
- "Memory after V4t : 1670.46 MB\n",
+ "Memory after V4t : 1669.24 MB\n",
"Rank 0: created area V4 with 0 local nodes\n",
- "Memory after V4 : 1697.47 MB\n",
+ "Memory after V4 : 1696.18 MB\n",
"Rank 0: created area VOT with 0 local nodes\n",
- "Memory after VOT : 1722.04 MB\n",
+ "Memory after VOT : 1720.76 MB\n",
"Rank 0: created area MSTd with 0 local nodes\n",
- "Memory after MSTd : 1742.13 MB\n",
+ "Memory after MSTd : 1740.80 MB\n",
"Rank 0: created area PIP with 0 local nodes\n",
- "Memory after PIP : 1763.51 MB\n",
+ "Memory after PIP : 1762.27 MB\n",
"Rank 0: created area PO with 0 local nodes\n",
- "Memory after PO : 1784.85 MB\n",
+ "Memory after PO : 1783.68 MB\n",
"Rank 0: created area DP with 0 local nodes\n",
- "Memory after DP : 1805.11 MB\n",
+ "Memory after DP : 1803.82 MB\n",
"Rank 0: created area MIP with 0 local nodes\n",
- "Memory after MIP : 1826.64 MB\n",
+ "Memory after MIP : 1825.39 MB\n",
"Rank 0: created area MDP with 0 local nodes\n",
- "Memory after MDP : 1848.14 MB\n",
+ "Memory after MDP : 1846.86 MB\n",
"Rank 0: created area VIP with 0 local nodes\n",
- "Memory after VIP : 1870.11 MB\n",
+ "Memory after VIP : 1868.78 MB\n",
"Rank 0: created area LIP with 0 local nodes\n",
- "Memory after LIP : 1894.00 MB\n",
+ "Memory after LIP : 1892.83 MB\n",
"Rank 0: created area PITv with 0 local nodes\n",
- "Memory after PITv : 1919.32 MB\n",
+ "Memory after PITv : 1918.03 MB\n",
"Rank 0: created area PITd with 0 local nodes\n",
- "Memory after PITd : 1944.49 MB\n",
+ "Memory after PITd : 1943.21 MB\n",
"Rank 0: created area MSTl with 0 local nodes\n",
- "Memory after MSTl : 1965.82 MB\n",
+ "Memory after MSTl : 1964.70 MB\n",
"Rank 0: created area CITv with 0 local nodes\n",
- "Memory after CITv : 1984.64 MB\n",
+ "Memory after CITv : 1983.83 MB\n",
"Rank 0: created area CITd with 0 local nodes\n",
- "Memory after CITd : 2003.97 MB\n",
+ "Memory after CITd : 2003.29 MB\n",
"Rank 0: created area FEF with 0 local nodes\n",
- "Memory after FEF : 2025.31 MB\n",
+ "Memory after FEF : 2024.62 MB\n",
"Rank 0: created area TF with 0 local nodes\n",
- "Memory after TF : 2040.98 MB\n",
+ "Memory after TF : 2040.30 MB\n",
"Rank 0: created area AITv with 0 local nodes\n",
- "Memory after AITv : 2063.69 MB\n",
+ "Memory after AITv : 2062.89 MB\n",
"Rank 0: created area FST with 0 local nodes\n",
- "Memory after FST : 2080.29 MB\n",
+ "Memory after FST : 2079.61 MB\n",
"Rank 0: created area 7a with 0 local nodes\n",
- "Memory after 7a : 2101.50 MB\n",
+ "Memory after 7a : 2100.93 MB\n",
"Rank 0: created area STPp with 0 local nodes\n",
- "Memory after STPp : 2120.32 MB\n",
+ "Memory after STPp : 2119.64 MB\n",
"Rank 0: created area STPa with 0 local nodes\n",
- "Memory after STPa : 2139.45 MB\n",
+ "Memory after STPa : 2138.77 MB\n",
"Rank 0: created area 46 with 0 local nodes\n",
- "Memory after 46 : 2154.82 MB\n",
+ "Memory after 46 : 2154.10 MB\n",
"Rank 0: created area AITd with 0 local nodes\n",
- "Memory after AITd : 2177.44 MB\n",
+ "Memory after AITd : 2176.68 MB\n",
"Rank 0: created area TH with 0 local nodes\n",
- "Memory after TH : 2190.15 MB\n",
- "Created areas and internal connections in 2.25 seconds.\n",
- "Created cortico-cortical connections in 22.48 seconds.\n",
- "Simulated network in 93.45 seconds.\n"
+ "Memory after TH : 2189.35 MB\n",
+ "Created areas and internal connections in 2.19 seconds.\n",
+ "Created cortico-cortical connections in 22.55 seconds.\n",
+ "Simulated network in 80.08 seconds.\n"
]
}
],
@@ -766,7 +766,7 @@
"1. Schmidt M, Bakker R, Shen K, Bezgin B, Diesmann M & van Albada SJ (2018)\n",
" A multi-scale layer-resolved spiking network model of\n",
" resting-state dynamics in macaque cortex. PLOS Computational Biology, 14(9): e1006359. [https://doi.org/10.1371/journal.pcbi.1006359](https://doi.org/10.1371/journal.pcbi.1006359) <br>\n",
- " **Fig 5. Resting state of the model with χ =1.9**"
+ " **Fig 3. Ground state of the model.**"
]
},
{