Changes for page SGA3 D1.2 Showcase 1

Last modified by fousekjan on 2022/07/04 18:31
From version 19.1
edited by fousekjan
on 2022/02/10 12:08
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To version 27.1
edited by fousekjan
on 2022/02/18 08:20
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19 19  The Jupyter notebooks in this collab will load all required Python modules including Siibra and The Virtual Brain, and the interfaces for launching the computationally demanding parts in the HPC infrastructure.
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21 -Running the notebooks requires an EBRANS account with permissions to access the Lab and programmatic access to the Knowledge Graph API. In addition, to interact with the HPC infrastructure, the user needs access to an active allocation on the corresponding FENIX site.
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25 +Running the notebooks requires an EBRANS account with permissions to access the Lab and programmatic access to the Knowledge Graph API. In addition, to interact with the HPC infrastructure, the user needs access to an active allocation on the corresponding FENIX site. Lastly, the virtual ageing brain notebooks write data to the Bucket storage—please make a private working copy of this Collab using the notebook [[copy_showcase1_collab.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/copy_showcase1_collab.ipynb]]. If you encounter any issues running the notebooks, please contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
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22 22  
23 23  == Simulation of resting-state activity ==
24 24  
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69 69  
70 70  Link to the notebook:
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72 -* [[regional_variability/notebooks/1_data_setup.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/1_data_setup.ipynb]]
78 +* [[regional_variability/notebooks/1_load_data.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/1_load_data.ipynb]]
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74 74  (% style="text-align:center" %)
75 -[[image:image-20220103095424-1.png]]
81 +[[image:download - 2022-02-10T130815.902.png||alt="region-wise gene expression heterogeneity"]]
76 76  
77 77  == Fitting model parameters for models with regional bias ==
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80 80  
81 81  Link to the notebook:
82 82  
83 -* [[regional_variability/notebooks/2_parameter_swep_proto.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/2_parameter_swep_proto.ipynb]]
89 +* [[regional_variability/notebooks/2_parameter_swep.ipynb>>https://lab.ch.ebrains.eu/hub/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/regional_variability/notebooks/2_parameter_swep.ipynb]]
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85 -[[image:image-20220103095948-1.png]]
91 +[[image:download - 2022-02-10T131102.033.png||alt="regional bias vs goodness of fit"]]
86 86  )))
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