Attention: The Collaboratory IAM will down for up to 1 hour on today, the 8th of July 2025 starting from 4.30pm CEST (my timezone) for up to 1 hour. Any and all services, which require a user login with an EBRAINS account, will be un-available during that time

Warning: The EBRAINS Drive and EBRAINS Lab will down on Tuesday, the 8th of July 2025 starting from 5pm CEST (my timezone) for up to 1 hour.


Last modified by abonard on 2025/05/23 13:23
From version 25.1
edited by jessicamitchell
on 2023/09/11 11:44
Change comment: There is no comment for this version
To version 3.1
edited by adavison
on 2023/01/25 11:45
Change comment: There is no comment for this version

Summary

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Title
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1 -Tools and services tutorials
1 +Tutorial Index
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1 -Collabs.documentation.WebHome
1 +Main.WebHome
Author
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1 -XWiki.jessicamitchell
1 +XWiki.adavison
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1 +This page is in development. Once ready it will be moved to a public location.
1 1  
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 -)))
3 +== Arbor ==
7 7  
8 -Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
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"]]
9 9  
10 -=== Brain atlases ===
19 +== Electrophysiology Analysis Toolkit ==
11 11  
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]]**
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"]]
21 21  
22 -=== Data analysis ===
29 +== PyNN ==
23 23  
24 -**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
25 -**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
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"]]
26 26  
27 -=== Simulation ===
34 +== VoluBA ==
28 28  
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]]**
36 +* [[Day 2 - 02. VoluBA (Sebastian Bludau)>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]]
39 39  
40 -=== Neurorobotics ===
38 +== The Virtual Brain ==
41 41  
42 -**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
43 -
44 -=== Medical data analytics ===
45 -
46 -**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
47 -
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"]]