Warning:  Due to planned infrastructure maintenance, the EBRAINS Wiki and EBRAINS Support system will be unavailable for up to three days starting Monday, 14 July. During this period, both services will be inaccessible, and any emails sent to the support address will not be received.

Attention: The EBRAINS Chat will down on Thursday, the 10th of July 2025 starting from 18.00pm CEST (my timezone) for up to 1 hour. 

Warning: The EBRAINS Drive, EBRAINS Bucket and EBRAINS Lab will down today, Wednesday, the 9th of July 2025 starting from 19:30 CEST (my timezone) for up to 1 hour.


Changes for page SGA3 D1.5 Showcase 1

Last modified by gorkazl on 2023/11/13 14:27
From version 23.1
edited by gorkazl
on 2023/11/13 14:27
Change comment: There is no comment for this version
To version 18.1
edited by gorkazl
on 2023/10/31 21:13
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -77,6 +77,7 @@
77 77  
78 78  * [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
79 79  
80 +(% class="wikigeneratedid" %)
80 80  == ==
81 81  
82 82  == b. Regional variability – Receptor density maps ==
... ... @@ -93,19 +93,18 @@
93 93  
94 94  The three datasets are characterised in the same parcellation. Link to the notebook:
95 95  
96 -* [[regional_variability/1_load_fMRI_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/1_load_fMRI_data.ipynb]]
97 -* [[regional_variability/2_retrieve_receptor_maps.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/2_retrieve_receptor_maps.ipynb]]
97 +* [[regional_variability/1_load_fMRI_data.ipynb>>https://drive.ebrains.eu/smart-link/792e61b8-f1d3-4fa3-84b9-5d60574c0891/]]
98 +* [[regional_variability/2_load_receptor_maps.ipynb>>https://drive.ebrains.eu/smart-link/0124a82b-0212-41f2-aa84-bbcc59a824d4/]]
98 98  
99 99  [[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T130815.902.png?rev=1.1||alt="region-wise gene expression heterogeneity"]]
100 100  
101 101  === Fitting model parameters with regional bias ===
102 102  
103 -A series of simulations of the whole-brain network model are launched in the EBRAINS HPC facilities in order to identify the optimal model parameters leading to simulated resting-state brain activity that best resembles the empirically observed activity. In this branch of the showcase, brain regions are simulated using the mean-field AdEx population model; specifically modified to account for the regional densities of GABAa and AMPA neuroreceptors. We provide two versions of the calculations, developed during the course of SGA3 of the HBP, in order to accelerate vast parametric sweeps over standard TVB simulation. The first employs the "RateML" to run TVB simulation on GPUs and the second is based on a novel TVB backend running on C++.
104 +A series of simulations of the whole-brain network model are launched in the EBRAINS HPC facilities in order to identify the optimal model parameters leading to simulated resting-state brain activity that best resembles the empirically observed activity. In this branch of the showcase, brain regions are simulated using the mean-field AdEx population model; specifically modified to account for the regional densities of GABAa and AMPA neuroreceptors. See the details in the following document.
104 104  
105 -Link to the notebooks:
106 +Link to the notebook:
106 106  
107 -* [[regional_variability/notebooks/3a_vast_paramsweep_GPU.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/3a_vast_paramsweep_GPU.ipynb]]
108 -* [[regional_variability/notebooks/3b_vast_paramsweep_TVBCpp.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/3b_vast_paramsweep_TVBCpp.ipynb]]
108 +* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.5%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
109 109  
110 110  [[image:https://wiki.ebrains.eu/bin/download/Collabs/sga3-d1-2-showcase-1/WebHome/download%20-%202022-02-10T131102.033.png?rev=1.1||alt="regional bias vs goodness of fit"]]
111 111  )))