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1		-Tutorial Index
	1	+Tools and services tutorials

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1		-Main.WebHome
	1	+Collabs.documentation.WebHome

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1		-XWiki.adavison
	1	+XWiki.jessicamitchell

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1		-This page is in development. Once ready it will be moved to a public location.
2	2
3		-~== Arbor ==
	2	+(% class="box infomessage" id="welcome" style="text-align: center;" %)
	3	+(((
	4	+Welcome to the single entry point to tutorials for EBRAINS tools and services.
	5	+Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.
	6	+)))
4	4
5		-~* ~[~[Arbor: A detailed single cell model>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]]
6		-~* ~[~[Arbor: A detailed single cell recipe>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]]
7		-~* ~[~[Arbor: A ring network>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]]
8		-~* ~[~[Arbor: A simple dendrite>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]]
9		-~* ~[~[Arbor: A simple single cell model>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]]
10		-~* ~[~[Arbor: A simple single cell recipe>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]]
11		-~* ~[~[Arbor: A single cell model from the Allen Brain Atlas>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_allen.html||rel="noopener noreferrer" target="_blank"]]
12		-~* ~[~[Arbor: A single cell model from the BluePyOpt Cell Optimisation Library>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_bluepyopt.html||rel="noopener noreferrer" target="_blank"]]
13		-~* ~[~[Arbor: Distributed ring network (MPI)>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]]
14		-~* ~[~[Arbor: Extracellular signals (LFPykit)>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]]
15		-~* ~[~[Arbor: GPU and profiling>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]]
16		-~* ~[~[Arbor: Spike Timing-dependent Plasticity Curve>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]]
17		-~* ~[~[Arbor: Two cells connected via a gap junction>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel="noopener noreferrer" target="_blank"]]
	8	+Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
18	18
19		-~== Electrophysiology Analysis Toolkit ==
	10	+=== Brain atlases ===
20	20
21		-~* ~[~[ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/asset.html||rel="noopener noreferrer" target="_blank"]]
22		-~* ~[~[Gaussian Process Factor Analysis>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]]
23		-~* ~[~[Parallel>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]]
24		-~* ~[~[Spike Pattern Detection and Evaluation (SPADE)>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]]
25		-~* ~[~[Statistics of spike trains>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]]
26		-~* ~[~[The Unitary Events Analysis>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]]
27		-~* ~[~[Time-domain Granger Causality>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]]
	12	+**[[ilastik>>doc:.ilastik.WebHome]]**
	13	+**[[LocaliZoom>>doc:.LocaliZoom.WebHome]]**
	14	+**[[MeshView>>doc:.MeshView.WebHome]]**
	15	+**[[Nutil>>doc:.Nutil.WebHome]]**
	16	+**[[QuickNII>>doc:.QuickNII.WebHome]]**
	17	+**[[VisuAlign>>doc:.VisuAlign.WebHome]]**
	18	+**[[voluba - Volumetric Brain Anchoring>>doc:.voluba - Volumetric Brain Anchoring.WebHome]]**
	19	+**[[WebAlign>>doc:.WebAlign.WebHome]]**
	20	+**[[WebWarp>>doc:.WebWarp.WebHome]]**
28	28
29		-~== PyNN ==
	22	+=== Data analysis ===
30	30
31		-~* ~[~[Building and simulating a simple model>>https:~/~/youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]]
32		-~* ~[~[Installing PyNN on a Linux system>>https:~/~/youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]]
	24	+**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
	25	+**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
33	33
34		-~== VoluBA ==
	27	+=== Simulation ===
35	35
36		-~* ~[~[Day 2 - 02. VoluBA (Sebastian Bludau)>>https:~/~/youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]]
	29	+**[[Arbor>>doc:.Arbor.WebHome]]**
	30	+**[[Arbor GUI>>doc:.Arbor GUI.WebHome]]**
	31	+**[[BluePyMM>>doc:.BluePyMM.WebHome]]**
	32	+**[[BluePyOpt>>doc:.BluePyOpt.WebHome]]**
	33	+**[[Hodgkin Huxley Neuron Builder>>doc:.Hodgkin Huxley Neuron Builder.WebHome]]**
	34	+**[[NEST Simulator>>doc:.NEST Simulator.WebHome]]**
	35	+**[[NESTML>>doc:.NESTML.WebHome]]**
	36	+**[[Neuron>>doc:.Neuron.WebHome]]**
	37	+**[[PyNN>>doc:.PyNN.WebHome]]**
	38	+**[[The Virtual Brain>>doc:.The Virtual Brain.WebHome]]**
37	37
38		-~== The Virtual Brain ==
	40	+=== Neurorobotics ===
39	39
40		-~* ~[~[TVB: Brain stimulation in The Virtual Brain>>https:~/~/youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]]
41		-~* ~[~[TVB: Building Your Own Brain Network Model>>https:~/~/docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]]
42		-~* ~[~[TVB: Clinical Applications - Stroke Recovery & Dementia>>https:~/~/youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]]
43		-~* ~[~[TVB: Evoked Responses in the Visual Cortex>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel="noopener noreferrer" target="_blank"]]
44		-~* ~[~[TVB: Exploring a model>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]]
45		-~* ~[~[TVB: Getting Started>>https:~/~/docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]]
46		-~* ~[~[TVB: Hands-On: Modeling stroke brain>>https:~/~/youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]]
47		-~* ~[~[TVB: Human Brain Project (HBP) TVB-NEST co-simulation>>https:~/~/youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]]
48		-~* ~[~[TVB: Import Virtual Brain ready data into TVB and create a brain model>>https:~/~/youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]]
49		-~* ~[~[TVB: Integrated workflows: Image processing pipeline>>https:~/~/youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]]
50		-~* ~[~[TVB: Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https:~/~/youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]]
51		-~* ~[~[TVB: Modeling Epilepsy>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]]
52		-~* ~[~[TVB: Modelling Epilepsy with The Virtual Brain>>https:~/~/youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]]
53		-~* ~[~[TVB: My first simulation with The Virtual Brain>>https:~/~/youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]]
54		-~* ~[~[TVB: Population Models in The Virtual Brain (TVB) and the Phase Plane>>https:~/~/youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]]
55		-~* ~[~[TVB: Region simulation tutorial>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]]
56		-~* ~[~[TVB: Resting State Networks>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]]
57		-~* ~[~[TVB: Simulating The Virtual Mouse Brain (TVMB)>>https:~/~/youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]]
58		-~* ~[~[TVB: Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https:~/~/youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]]
59		-~* ~[~[TVB: Surface simulation tutorial>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]]
60		-~* ~[~[TVB: Surface-based simulations and deep brain stimulations>>https:~/~/youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]]
61		-~* ~[~[TVB: The Bayesian Virtual Epileptic Patient (BVEP)>>https:~/~/youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]]
62		-~* ~[~[TVB: TVB to NEST multi-scale simulation>>https:~/~/youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]]
	42	+**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
	43	+
	44	+=== Medical data analytics ===
	45	+
	46	+**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
	47	+