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Summary

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Title
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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 -This page is in development. Once ready it will be moved to a public location.
1 +(% class="box infomessage" id="welcome" style="text-align: center;" %)
2 +(((
3 +Welcome to the single entry point to tutorials for EBRAINS tools and services.
4 +Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.
5 +)))
2 2  
3 -== Arbor ==
7 +Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
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"]]
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 +**[[VoluBA>>doc:.VoluBA.WebHome]]**
28 28  
29 -== PyNN ==
14 +=== 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"]]
16 +**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
17 +**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
18 +**[[ilastik>>doc:.ilastik.WebHome]]**
33 33  
34 -== VoluBA ==
20 +=== Simulation ===
35 35  
36 -* [[Day 2 - 02. VoluBA (Sebastian Bludau)>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]]
22 +**[[Arbor>>doc:.Arbor.WebHome]]**
23 +**[[BluePyMM>>doc:.BluePyMM.WebHome]]**
24 +**[[BluePyOpt>>doc:.BluePyOpt.WebHome]]**
25 +**[[Hodgkin Huxley Neuron Builder>>doc:.Hodgkin Huxley Neuron Builder.WebHome]]**
26 +**[[NEST>>doc:.NEST.WebHome]]**
27 +**[[NESTML>>doc:.NESTML.WebHome]]**
28 +**[[Neuron>>doc:.Neuron.WebHome]]**
29 +**[[PyNN>>doc:.PyNN.WebHome]]**
30 +**[[The Virtual Brain>>doc:.The Virtual Brain.WebHome]]**
37 37  
38 -== The Virtual Brain ==
32 +=== 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"]]
34 +**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
35 +
36 +=== Medical data analytics ===
37 +
38 +**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**