Changes for page SGA3 D1.5 Showcase 1

Last modified by gorkazl on 2023/11/13 14:27
From version 18.1
edited by gorkazl
on 2023/10/31 21:13
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To version 22.1
edited by gorkazl
on 2023/11/13 14:25
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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]]
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80 -(% class="wikigeneratedid" %)
81 81  == ==
82 82  
83 83  == b. Regional variability – Receptor density maps ==
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94 94  
95 95  The three datasets are characterised in the same parcellation. Link to the notebook:
96 96  
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/]]
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]]
99 99  
100 100  [[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"]]
101 101  
102 102  === Fitting model parameters with regional bias ===
103 103  
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.
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++.
105 105  
106 -Link to the notebook:
105 +Link to the notebooks:
107 107  
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]]
107 +* [[regional_variability/notebooks/3a_vast_paramsweep_GPU.ipynb>>https://drive.ebrains.eu/smart-link/73ef88f7-0ce4-4b01-a083-f65a40514f5d/]]
108 +* [[regional_variability/notebooks/3b_vast_paramsweep_TVBCpp.ipynb>>https://drive.ebrains.eu/smart-link/31f9e2dd-6576-4fa8-805d-76f47906c04e/]]
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  )))