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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	+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.
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17		-An EBRAINS collab (as this one dedicated to the SGA3 D1.5 Deliverable) is a virtual environment providing access to a few interlinked services: Wiki, Drive, Bucket and Lab. The //Wiki// is this web interface that allows to visually navigate through the components of a collab and allows for basic documentation to be presented in the form of webpages. The //Drive// provides storage for small files. It is the local filesystem of a collab in which the documentation, the notebooks and all the supporting code are placed. The //Bucket// is a storage service for larger files. In the present collab, the Bucket holds the pre-computed results from the extensive parameter sweeps and model optimizations to allow skipping the computationally demanding steps. The //Lab// service is an instance of JupyterLab—an interactive computing environment—where the notebooks can be run and worked with. The Lab displays the code and the Notebooks that are stored in the Drive.
	17	+An EBRAINS collab (as this one dedicated to the SGA3 D1.5 Deliverable) is a virtual environment providing access to a few interlinked services: Wiki, Drive, Bucket and Lab. The //Wiki// is this web interface that allows to visually navigate through the components of a collab and allows for basic documentation to be presented in the form of webpages. The //Drive// provides storage for small files. It is the local filesystem of a collab in which the documentation, the notebooks and all the supporting code are placed. The //Bucket// is a storage service for larger files. In the present collab, the Bucket holds the pre-computed results from the extensive parameter sweeps and model optimizations to allow skipping the computationally demanding steps. The //Lab// service is an instance of JupyterLab—an interactive computing environment—where the notebooks can be run and worked with. The Lab displays the code and the notebooks that are stored in the Drive.
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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.
	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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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]].
	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.
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	27	+Please, to avoid overwriting precomputed data, //**make first a private working duplicate**// 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, contact [[The Virtual Brain Facility Hub>>mailto:jan.fousek@univ-amu.fr]].
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30		-The virtual ageing study is described in detail in following publication:
	32	+The Showcase 1 aimed at investigations related to variability in neuroscience from two perspectives: (a) the interpersonal variability studied by the virtual ageing study, and (b) the variability across different cortical regions within an individual brain.
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	34	+(% class="wikigeneratedid" %)
	35	+== (a) Interpersonal variability—virtual ageing ==
	36	+
	37	+(% class="wikigeneratedid" %)
	38	+See the details of the first study in the following publication:
	39	+
32	32	M. Lavanga, J. Stumme, B. H. Yalcinkaya, J. Fousek, C. Jockwitz, H. Sheheitli, N. Bittner, M. Hashemi, S. Petkoski, S. Caspers, and V. Jirsa, [[The Virtual Aging Brain: A Model-Driven Explanation for Cognitive Decline in Older Subjects>>https://doi.org/10.1101/2022.02.17.480902]].
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34		-== Simulation of resting-state activity ==
	42	+=== Simulation of resting-state activity ===
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36	36	The fist notebook in the inter-individual variability workflow explores the resting-state simulation for a subject of the 1000BRAINS dataset. Functional data are simulated by means of a brain network model implemented in TVB, which is an ensemble of neural mass models linked via the weights of the structural connectivity (SC) matrix. Following topics are covered:
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47	47	[[image:image-20220103100841-2.png]]
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49		-== Virtual ageing trajectories ==
	57	+=== Virtual ageing trajectories ===
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51	51	The second steps shows the investigation of virtual ageing trajectory for each subject. In this context, we are going to show:
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61	61	[[image:image-20220103101022-3.png]]
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63		-== Inference with SBI ==
	71	+=== Inference with SBI ===
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65	65	The last step of the inter-individual variability workflow employs Simulation Based Inference for estimation of the full posterior values of the parameters. Here, a deep neural estimator is trained to provide a relationship between the parameters of a model (black box simulator) and selected descriptive statistics of the observed data.
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71	71	* [[virtual_ageing/notebooks/3_inference_with_SBI.ipynb>>https://lab.ch.ebrains.eu/user-redirect/lab/tree/shared/SGA3%20D1.2%20Showcase%201/virtual_ageing/notebooks/3_inference_with_SBI.ipynb]]
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73		-== Regional variability data ==
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	82	+== (b) Regional variability ==
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	84	+Aims at demonstrating the construction of whole-brain network models of the brain's activity accounting for differences in receptor densities across cortical regions.
	85	+
	86	+=== Loading the data from EBRAINS via the //siibra// interface ===
	87	+
75	75	The first step of the regional variability workflow consists in loading the data from the Knowledge Graph, including the regional bias on the model. In this case we require:
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77	77	1. Structural connectivity matrices,