Attention: The Collaboratory IAM will down for up to 1 hour on Monday, the 7th of July 2025 starting from 5pm 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


Last modified by abonard on 2025/05/23 13:23
From version 4.1
edited by adavison
on 2023/01/25 12:35
Change comment: There is no comment for this version
To version 21.1
edited by adavison
on 2023/02/27 16:46
Change comment: There is no comment for this version

Summary

Details

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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
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 ==
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)
11 +=== Brain atlases ===
28 28  
29 -== PyNN ==
13 +|**[[VoluBA>>doc:.VoluBA.WebHome]]**
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)
33 33  
34 -== The Virtual Brain ==
16 +=== Data analysis ===
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)
18 +|**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
19 +|**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
20 +|**[[ilastik>>doc:.ilastik.WebHome]]**
61 61  
62 -== VoluBA ==
63 63  
64 -* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel=" noopener noreferrer" target="_blank"]] (-)
23 +=== Simulation ===
24 +
25 +|**[[Arbor>>doc:.Arbor.WebHome]]**
26 +|**[[BluePyMM>>doc:.BluePyMM.WebHome]]**
27 +|**[[BluePyOpt>>doc:.BluePyOpt.WebHome]]**
28 +|**[[Hodgkin Huxley Neuron Builder>>doc:.Hodgkin Huxley Neuron Builder.WebHome]]**
29 +|**[[NEST>>doc:.NEST.WebHome]]**
30 +|**[[NESTML>>doc:.NESTML.WebHome]]**
31 +|**[[Neuron>>doc:.Neuron.WebHome]]**
32 +|**[[PyNN>>doc:.PyNN.WebHome]]**
33 +|**[[The Virtual Brain>>doc:.The Virtual Brain.WebHome]]**
34 +
35 +
36 +=== Neurorobotics ===
37 +
38 +|**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
39 +
40 +
41 +=== Medical data analytics ===
42 +
43 +|**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
44 +