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 26.1
edited by abonard
on 2025/04/10 15:19
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To version 4.1
edited by adavison
on 2023/01/25 12:35
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Summary

Details

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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.abonard
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 +* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] (beginner)
6 +* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
7 +* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
8 +* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
9 +* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
10 +* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
11 +* [[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"]] (advanced)
12 +* [[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"]] (advanced)
13 +* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
14 +* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
15 +* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
16 +* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
17 +* [[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"]] (advanced)
9 9  
10 -=== **Atlases** ===
19 +== Electrophysiology Analysis Toolkit ==
11 11  
12 -**[[ilastik>>doc:.ilastik.WebHome]]**
13 -**[[Julich-Brain Cytoarchitectonic Atlas>>doc:.Julich-Brain Cytoarchitectonic Atlas.WebHome]]**
14 -**[[LocaliZoom>>doc:.LocaliZoom.WebHome]]**
15 -**[[MeshView>>doc:.MeshView.WebHome]]**
16 -**[[Nutil>>doc:.Nutil.WebHome]]**
17 -**[[QuickNII>>doc:.QuickNII.WebHome]]**
18 -**[[siibra-explorer>>doc:.siibra-explorer.WebHome]]**
19 -**[[siibra-python>>doc:.siibra-python.WebHome]]**
20 -**[[VisuAlign>>doc:.VisuAlign.WebHome]]**
21 -**[[voluba - Volumetric Brain Anchoring>>doc:.voluba - Volumetric Brain Anchoring.WebHome]]**
22 -**[[WebAlign>>doc:.WebAlign.WebHome]]**
23 -**[[WebWarp>>doc:.WebWarp.WebHome]]**
21 +* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel=" noopener noreferrer" target="_blank"]] (beginner)
22 +* [[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"]] (advanced)
23 +* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
24 +* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
25 +* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
26 +* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
27 +* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
24 24  
25 -=== **Medical Analytics** ===
29 +== PyNN ==
26 26  
27 -**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
28 -**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
31 +* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel=" noopener noreferrer" target="_blank"]] (beginner)
32 +* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel=" noopener noreferrer" target="_blank"]] (beginner)
29 29  
30 -=== **Modelling and Simulation** ===
34 +== The Virtual Brain ==
31 31  
32 -**[[Arbor>>doc:.Arbor.WebHome]]**
33 -**[[Arbor GUI>>doc:.Arbor GUI.WebHome]]**
34 -**[[BluePyMM>>doc:.BluePyMM.WebHome]]**
35 -**[[BluePyOpt>>doc:.BluePyOpt.WebHome]]**
36 -**[[BrainScaleS Operating System>>doc:.BrainScaleS Operating System.WebHome]]**
37 -**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
38 -**[[Hodgkin Huxley Neuron Builder>>doc:.Hodgkin Huxley Neuron Builder.WebHome]]**
39 -**[[Local Field Potentials in Python>>doc:.Local Field Potentials in Python.WebHome]]**
40 -**[[NEST Desktop>>doc:.NEST Desktop.WebHome]]**
41 -**[[NEST Simulator>>doc:.NEST Simulator.WebHome]]**
42 -**[[NESTML>>doc:.NESTML.WebHome]]**
43 -**[[Neuron>>doc:.Neuron.WebHome]]**
44 -**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
45 -**[[PyNN>>doc:.PyNN.WebHome]]**
46 -**[[SpiNNaker Jupyter service>>doc:.SpiNNaker Jupyter service.WebHome]]**
47 -**[[sPyNNaker>>doc:.sPyNNaker.WebHome]]**
48 -**[[The Virtual Brain>>doc:.The Virtual Brain.WebHome]]**
49 -**[[ViSimpl>>doc:.ViSimpl.WebHome]]**
36 +* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] (beginner)
37 +* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] (beginner)
38 +* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] (beginner)
39 +* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] (beginner)
40 +* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] (advanced)
41 +* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] (advanced)
42 +* [[Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
43 +* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
44 +* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] (advanced)
45 +* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] (advanced)
46 +* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] (advanced)
47 +* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] (advanced)
48 +* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] (advanced)
49 +* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
50 +* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] (advanced)
51 +* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
52 +* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
53 +* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] (advanced)
54 +* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] (advanced)
55 +* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
56 +* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] (advanced)
57 +* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] (advanced)
58 +* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] (advanced)
59 +* [[TVB: Modeling Epilepsy>>https://docs.thevirtualbrain.org/tutorials/tutorial_3_ModelingEpilepsy.html#tutorial-3-modelingepilepsy||rel=" noopener noreferrer" target="_blank"]] (advanced)
60 +* [[TVB: Resting State Networks>>https://docs.thevirtualbrain.org/tutorials/tutorial_2_RestingStateNetworks.html#tutorial-2-restingstatenetworks||rel=" noopener noreferrer" target="_blank"]] (advanced)
50 50  
51 -=== **FAIR data** ===
62 +== VoluBA ==
52 52  
53 -**[[(Dataset) Excitability of mouse hippocampal CA1 pyramidal neurons during sustained (500 ms) strong depolarization>>doc:.(Dataset) Excitability of mouse hippocampal CA1 pyramidal neurons during sustained (500 ms) strong depolarization.WebHome]]**
54 -**[[(Dataset) Excitability profile of CA1 pyramidal neurons in APPPS1 Alzheimer disease mice and control littermates>>doc:.(Dataset) Excitability profile of CA1 pyramidal neurons in APPPS1 Alzheimer disease mice and control littermates.WebHome]]**
55 -**[[EBRAINS Knowledge Graph>>doc:.EBRAINS Knowledge Graph.WebHome]]**
56 -**[[EBRAINS Live Papers Builder>>doc:.EBRAINS Live Papers Builder.WebHome]]**
57 -**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
58 -
59 -=== **Computing Infrastructure** ===
60 -
61 -**[[SpiNNaker Jupyter service>>doc:.SpiNNaker Jupyter service.WebHome]]**
62 -
63 -=== **Miscellaneous** ===
64 -
65 -**[[EBRAINS Live Papers Viewer>>doc:.EBRAINS Live Papers Viewer.WebHome]]**
66 -
67 -
68 -**Miscellaneous tutorials**
69 -
70 -**[[IPR, exploitation and translation of research - Lecture 7: Looking into the future using emerging trends: What are they and how do we identify them? Part 1>>https://www.youtube.com/watch?v=8j6klXkSv0s&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=13||rel=" noopener noreferrer" target="_blank"]]**
71 -**Level**: beginner(%%) **Type**: video presentation
72 -
73 -**[[Innovation management: Innovation management tools in the HBP and EBRAINS context - Part 2>>https://www.youtube.com/watch?v=9IUMUkrH_Vs&list=PLvAS8zldX4CjlNfu4tEIPc6uKWGzglHei||rel=" noopener noreferrer" target="_blank"]]**
74 -**Level**: beginner(%%) **Type**: video presentation
75 -
76 -**[[Technology Readiness Level Assessment Course>>https://www.humanbrainproject.eu/en/collaborate-hbp/innovation-industry/trl-assessment-course/||rel=" noopener noreferrer" target="_blank"]]**
77 -**Level**: beginner(%%) **Type**: video presentation
78 -
79 -**[[IPR, exploitation and translation of research course - Lecture 5: New innovation models at the interface between academia and industry Part 2>>https://www.youtube.com/watch?v=iwTiZpRe9LE&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=9||rel=" noopener noreferrer" target="_blank"]]**
80 -**Level**: beginner(%%) **Type**: video presentation
81 -
82 -**[[IRP, exploitaiton and translation of research course - Lecture 3: Basic elements in the patenting world Part 1>>https://www.youtube.com/watch?v=Ii-bJlLOhyE&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=5||rel=" noopener noreferrer" target="_blank"]]**
83 -**Level**: -(%%) **Type**: video presentation
84 -
85 -**[[IPR, exploitation and translation of research course - Lecture 5: New innovation models at the interface between academia and industry Part 1>>https://www.youtube.com/watch?v=iwTiZpRe9LE&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=9||rel=" noopener noreferrer" target="_blank"]]**
86 -**Level**: beginner(%%) **Type**: video presentation
87 -
88 -**[[Intellectual Property Rights (IRP), translation & exploitation of research- Introduction to the courses>>https://www.youtube.com/watch?v=K6gvvRv289c&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu||rel=" noopener noreferrer" target="_blank"]]**
89 -**Level**: beginner(%%) **Type**: video presentation
90 -
91 -**[[IRP, exploitaiton and translation of research course - Lecture 1: Is your "Million Dollar Idea" a viable business concept?>>https://www.youtube.com/watch?v=W9kXSuQo9M0&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=3||rel=" noopener noreferrer" target="_blank"]]**
92 -**Level**: beginner(%%) **Type**: video presentation
93 -
94 -**[[IRP, exploitaiton and translation of research course - Lecture 2: Bottom-up research: The most critical skill in entrepreneurship>>https://www.youtube.com/watch?v=XZBMnUjelEQ&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=4||rel=" noopener noreferrer" target="_blank"]]**
95 -**Level**: beginner(%%) **Type**: video presentation
96 -
97 -**[[Innovation Funding Workshop>>https://youtu.be/JFxaoK2yMqI||rel=" noopener noreferrer" target="_blank"]]**
98 -**Level**: beginner(%%) **Type**: video tutorial
99 -
100 -**[[IPR, exploitation and translation of research course - Lecture 6: Transferring innovation from academy to industry Part 2>>https://www.youtube.com/watch?v=Js9-COrdFS0&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=12||rel=" noopener noreferrer" target="_blank"]]**
101 -**Level**: beginner(%%) **Type**: video presentation
102 -
103 -**[[IPR, exploitation and translation of research course - Lecture 4: Patents in the realm of neuroscience Part 2>>https://www.youtube.com/watch?v=ba9pQ3LqoHw&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu||rel=" noopener noreferrer" target="_blank"]]**
104 -**Level**: beginner(%%) **Type**: -
105 -
106 -**[[IRP, exploitaiton and translation of research course - Lecture 3: Basic elements in the patenting world Part 2>>https://www.youtube.com/watch?v=4TFb77VsmFQ&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=6||rel=" noopener noreferrer" target="_blank"]]**
107 -**Level**: beginner(%%) **Type**: video presentation
108 -
109 -**[[Plans for the exploitation of HBP technologies course>>https://www.humanbrainproject.eu/en/collaborate-hbp/innovation-industry/exploitation-plan-course/||rel=" noopener noreferrer" target="_blank"]]**
110 -**Level**: beginner(%%) **Type**: video tutorial
111 -
112 -**[[Key factors to successful exploitation of research results and technology transfer>>https://sos-ch-dk-2.exo.io/public-website-production/filer_public/47/7e/477eb33a-27ce-42f5-b4d3-620339864294/key_factors_innovation_and_tech_transfer.pdf||rel=" noopener noreferrer" target="_blank"]]**
113 -**Level**: beginner(%%) **Type**: slide deck
114 -
115 -**[[IPR, exploitation and translation of research - Lecture 7: Looking into the future using emerging trends: What are they and how do we identify them? Part 2>>https://www.youtube.com/watch?v=b0vOyHTW2Rc&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=14||rel=" noopener noreferrer" target="_blank"]]**
116 -**Level**: beginner(%%) **Type**: video presentation
117 -
118 -**[[IPR, exploitation and translation of research course - Lecture 4: Patents in the realm of neuroscience Part 1>>https://www.youtube.com/watch?v=8m-ucwJhtV4&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu||rel=" noopener noreferrer" target="_blank"]]**
119 -**Level**: beginner(%%) **Type**: video presentation
120 -
121 -**[[IPR, exploitation and translation of research course - Lecture 6: Transferring innovation from academy to industry Part 1>>https://www.youtube.com/watch?v=8FQzTR5aWA0&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=11||rel=" noopener noreferrer" target="_blank"]]**
122 -**Level**: beginner(%%) **Type**: video presentation
123 -
124 -**[[Innovation management: Innovation management tools in the HBP and EBRAINS context - Part 1>>https://www.youtube.com/watch?v=NNbwITmioEI&list=PLvAS8zldX4CjlNfu4tEIPc6uKWGzglHei||rel=" noopener noreferrer" target="_blank"]]**
125 -**Level**: beginner(%%) **Type**: video presentation
126 -
127 -
64 +* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel=" noopener noreferrer" target="_blank"]] (-)