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20	20	(((
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	24	+== The Virtual Brain at EBRAINS ==
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	26	+[[image:overview_figure_v6.pdf]][[image:Screenshot 2020-10-19 at 09.14.45.png]]
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23	23	== TVB pipeline: Extract connectomes ==
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25	25	As a first step we browse through The Knowledge Graph (KG) in order to find a suitable dataset to construct a brain model. The dataset must contain diffusion-weighted MRI data, in order to extract a structural connectome, which will form the basis of a brain network model. Structural connectivity extracted from diffusion MRI is used to quantify how strongly brain regions interact in the brain model. Next, the data set must contain functional MRI (fMRI) data, because a common approach is to tune the parameters of the brain model such that the simulated fMRI functional connectivity fits with the empirical fMRI data. For fitting, we usually compute functional connectivity matrices from simulated and empirical data. Finally, we need anatomical T1-weighted MRI to extract cortical surfaces and to perform a parcellation of the brain into different regions.
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46	46	== The Virtual Brain: Simulate brain activity ==
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48		-The Virtual Brain is the main TVB software package. It is a neuroinformatics platform that provides an ecosystem of tools for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivity. TVB can be operated via GUI and programmatic Python interface. On the HBP Collaboratory Platform TVB Simulator usage is introduced through IPython Notebooks. Additionally, the TVB GUI can be directly accessed as [[a Web App>>https://thevirtualbrain.apps.hbp.eu/user/profile]]. Via the Web App users can configure simulations that are – depending on their complexity – either simulated directly on the web server or on a supercomputer, thereby making resource-consuming TVB functionality accessible to researchers that do not have access to supercomputers. Compiled standalone versions of the main software package can be downloaded from thevirtualbrain.org. In the following we take you through the main steps of brain network model simulation.
	53	+The Virtual Brain is the main TVB software package. It is a neuroinformatics platform that provides an ecosystem of tools for simulating and analysing large-scale brain network dynamics based on biologically realistic connectivity. TVB can be operated via GUI and programmatic Python interface. On the EBRAINS Collaboratory Platform TVB Simulator usage is introduced through IPython Notebooks in the main TVB [[collab>>doc:Collabs.the-virtual-brain.WebHome||target="_blank"]]. Additionally, the TVB GUI can be directly accessed as [[a Web App>>https://thevirtualbrain.apps.hbp.eu/user/profile]]. Via the Web App users can configure simulations that are – depending on their complexity – either simulated directly on the web server or on a supercomputer, thereby making resource-consuming TVB functionality accessible to researchers that do not have access to supercomputers. Compiled standalone versions of the main software package can be downloaded from thevirtualbrain.org. In the following we take you through the main steps of brain network model simulation.
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50	50	* Construct and downloaded the structural connectivity generated with the TVB pipeline. Alternatively, you can use demo SC that is shipped with the main TVB package. Next, go to the TVB Collaboratory and work through the example “[[Load TVB Connectivity>>https://collab.humanbrainproject.eu/#/collab/1609/nav/15645]]”
51	51	* Having loaded the SC, next work through the basic process of setting up a simulation, see
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77	77	The EBRAINS Collaboratory “[[TVB C ~~-~~- High-speed parallel brain network models>>https://wiki.ebrains.eu/bin/view/Collabs/tvb-c-high-speed-parallel-brain-network-]]” explains how to use the container on supercomputer backends with a Jupyter notebook as frontend:
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79		-* Open the “[[TVB C ~~-~~- High-speed parallel brain network models>>https://wiki.ebrains.eu/bin/view/Collabs/tvb-c-high-speed-parallel-brain-network]]” Collab
	84	+* Open the “[[TVB C ~~-~~- High-speed parallel brain network models>>https://wiki.ebrains.eu/bin/view/Collabs/tvb-c-high-speed-parallel-brain-network-]]” Collab
80	80	* Follow the instructions in the Collab notebook or [[here>>https://hub.docker.com/r/thevirtualbrain/fast_tvb]] to set up a brain model, simulate it and collect the results.
81	81	* Simulations are more efficient when only a single thread is created, but faster for multiple threads. Play around with the num_threads parameter and compare the execution speeds for different settings. If execution speed is the primary goal a higher number of threads is advised, if efficiency during parameter space exploration is the goal, then it is advised to use multiple single-threaded instances of the program.
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