Summary

• Page properties (1 modified, 0 added, 0 removed)
• Attachments (0 modified, 1 added, 0 removed)
  • image-20220103095424-1.png

Details

Page properties

Content

...	...	@@ -12,13 +12,23 @@
12	12	(((
13	13	(% class="col-xs-12 col-sm-8" %)
14	14	(((
15		-== Virtual ageing trajectories: 1000BRAINS cohort ==
	15	+The Showcase is implemented as a series of interactive Jupyter notebooks covering the individual logical steps and can be accessed in a dedicated public EBRAINS collab.
16	16
17	17
18		-== Brain region variance: incorporating receptor densities ==
	18	+The EBRAINS collab consists of interlinked Drive, Bucket, Wiki, and Lab. The Drive provides small file storage and contains the notebooks and all supporting code. The Bucket is a large file storage service and holds the pre-computed results of the extensive parameter sweeps and model optimizations to allow skipping the computationally demanding steps. The documentation of the showcase implementation is collected in the Wiki. The Lab service is an instance of JupyterLab—an interactive computing environment where the notebooks can be run and worked with.
19	19
20	20
	21	+The 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. Running the notebooks requires an EBRANS account with permissions to access the Lab and the Knowledge Graph API. In addition, to be able to interact with the HPC infrastructure, the user has to have access to an active allocation on the corresponding FENIX site.
21	21
	23	+
	24	+== Regional variability data ==
	25	+
	26	+The first step of the regional variability workflow loads the data from the Knowledge Graph and defines the regional bias on the model. In this case we require: 1) structural connectivity matrices, 2) GABA and AMPA receptor densities at each region, and 3) empirical resting-state fMRI data for fitting and validation of the simulations. The three datasets shall be characterised in the same parcellation. The notebook can be found here: [[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]]
	27	+
	28	+(% style="text-align:center" %)
	29	+[[image:image-20220103095424-1.png]]
	30	+
	31	+
22	22	)))
23	23
24	24

image-20220103095424-1.png

Author

...	...	@@ -1,0 +1,1 @@
	1	+XWiki.fousekjan

Size

...	...	@@ -1,0 +1,1 @@
	1	+33.7 KB

Content