Changes for page SGA3 D1.2 Showcase 1

Last modified by fousekjan on 2022/07/04 18:31
From version 11.1
edited by fousekjan
on 2022/01/03 09:08
Change comment: Uploaded new attachment "image-20220103100841-2.png", version {1}
To version 3.1
edited by fousekjan
on 2021/12/17 09:02
Change comment: There is no comment for this version

Summary

Details

Page properties
Content
... ... @@ -2,9 +2,9 @@
2 2  (((
3 3  (% class="container" %)
4 4  (((
5 -= Advanced prototype software integrating heterogeneous region models =
5 += My Collab's Extended Title =
6 6  
7 -SGA3 D1.2 - Showcase 1: "Degeneracy in neuroscience - when is Big Data big enough"
7 +My collab's subtitle
8 8  )))
9 9  )))
10 10  
... ... @@ -12,35 +12,15 @@
12 12  (((
13 13  (% class="col-xs-12 col-sm-8" %)
14 14  (((
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.
15 += What can I find here? =
16 16  
17 +* Notice how the table of contents on the right
18 +* is automatically updated
19 +* to hold this page's headers
17 17  
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.
21 += Who has access? =
19 19  
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. 
22 -
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.
27 -
28 -Link to the notebook:
29 -
30 -* [[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]]
31 -
32 -(% style="text-align:center" %)
33 -[[image:image-20220103095424-1.png]]
34 -
35 -== Fitting model parameters for models with regional bias ==
36 -
37 -A series of simulations of the whole-brain network model is 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.
38 -
39 -Link to the notebook:
40 -
41 -* [[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]]
42 -
43 -[[image:image-20220103095948-1.png]]
23 +Describe the audience of this collab.
44 44  )))
45 45  
46 46  
... ... @@ -47,7 +47,7 @@
47 47  (% class="col-xs-12 col-sm-4" %)
48 48  (((
49 49  {{box title="**Contents**"}}
50 -{{toc start="2"/}}
30 +{{toc/}}
51 51  {{/box}}
52 52  
53 53  
image-20220103095424-1.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -33.7 KB
Content
image-20220103095948-1.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -4.1 KB
Content
image-20220103100841-2.png
Author
... ... @@ -1,1 +1,0 @@
1 -XWiki.fousekjan
Size
... ... @@ -1,1 +1,0 @@
1 -116.4 KB
Content
XWiki.XWikiRights[2]
Allow/Deny
... ... @@ -1,1 +1,0 @@
1 -Allow
Groups
... ... @@ -1,1 +1,0 @@
1 -Collabs.sga3-d1-2-showcase-1._.groups.collab-sga3-d1-2-showcase-1-administrator
Levels
... ... @@ -1,1 +1,0 @@
1 -view,comment,edit,delete