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 4.1
edited by adavison
on 2023/01/25 12:35
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To version 27.1
edited by abonard
on 2025/05/23 13:23
Change comment: There is no comment for this version

Summary

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Title
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1 -Tutorial Index
1 +Tools and services tutorials
Parent
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1 -Main.WebHome
1 +Collabs.documentation.WebHome
Author
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1 -XWiki.adavison
1 +XWiki.abonard
Content
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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 -* [[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)
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 +=== **Atlases** ===
20 20  
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)
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]]**
28 28  
29 -== PyNN ==
25 +=== **Medical Analytics** ===
30 30  
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)
27 +**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
28 +**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
33 33  
34 -== The Virtual Brain ==
30 +=== **Modelling and Simulation** ===
35 35  
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)
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]]**
61 61  
62 -== VoluBA ==
51 +=== **FAIR data** ===
63 63  
64 -* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel=" noopener noreferrer" target="_blank"]] (-)
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 +**[[Example Slide deck – 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"]]**
128 +**Level**: beginner(%%) **Type**: slide deck
129 +
130 +**[[IPR, exploitation and translation of research course - Lecture 5: New innovation models at the interface between academia and industry Part 1 (Copy)>>https://www.youtube.com/watch?v=iwTiZpRe9LE&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=9||rel=" noopener noreferrer" target="_blank"]]**
131 +**Level**: beginner(%%) **Type**: video presentation
132 +
133 +