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edited by abonard
on 2025/05/23 13:23
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on 2023/02/27 14:30
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1 -
2 2  (% class="box infomessage" id="welcome" style="text-align: center;" %)
3 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.
3 +Welcome to the single entry point to tutorials for EBRAINS tools and services. Here, you can find a list of EBRAINS offerings, sorted by topic, and links to their tutorials.
6 6  )))
7 7  
8 8  Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
9 9  
10 -=== **Atlases** ===
8 +== Arbor ==
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]]**
10 +* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner)
11 +* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] (advanced)
12 +* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)
13 +* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] (advanced)
14 +* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] (advanced)
15 +* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)
16 +* [[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)
17 +* [[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)
18 +* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] (advanced)
19 +* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] (advanced)
20 +* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] (advanced)
21 +* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced)
22 +* [[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)
24 24  
25 -=== **Medical Analytics** ===
24 +== Bids Manager & Pipeline ==
26 26  
27 -**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
28 -**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
26 +* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel="noopener noreferrer" target="_blank"]] (advanced)
29 29  
30 -=== **Modelling and Simulation** ===
28 +== BluePyMM ==
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]]**
30 +* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner)
50 50  
51 -=== **FAIR data** ===
32 +== BluePyOpt ==
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]]**
34 +* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner)
58 58  
59 -=== **Computing Infrastructure** ===
36 +== Brainstorm ==
60 60  
61 -**[[SpiNNaker Jupyter service>>doc:.SpiNNaker Jupyter service.WebHome]]**
38 +* [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel="noopener noreferrer" target="_blank"]] (beginner)
39 +* [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel="noopener noreferrer" target="_blank"]] (advanced)
40 +* [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel="noopener noreferrer" target="_blank"]] (advanced)
41 +* [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel="noopener noreferrer" target="_blank"]] (advanced)
42 +* [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel="noopener noreferrer" target="_blank"]] (advanced)
43 +* [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel="noopener noreferrer" target="_blank"]] (advanced)
44 +* [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel="noopener noreferrer" target="_blank"]] (advanced)
45 +* [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel="noopener noreferrer" target="_blank"]] (advanced)
46 +* [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel="noopener noreferrer" target="_blank"]] (advanced)
47 +* [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel="noopener noreferrer" target="_blank"]] (advanced)
48 +* [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel="noopener noreferrer" target="_blank"]] (advanced)
49 +* [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel="noopener noreferrer" target="_blank"]] (advanced)
50 +* [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel="noopener noreferrer" target="_blank"]] (advanced)
51 +* [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel="noopener noreferrer" target="_blank"]] (advanced)
52 +* [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel="noopener noreferrer" target="_blank"]] (advanced)
53 +* [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel="noopener noreferrer" target="_blank"]] (advanced)
54 +* [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel="noopener noreferrer" target="_blank"]] (advanced)
55 +* [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel="noopener noreferrer" target="_blank"]] (advanced)
56 +* [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel="noopener noreferrer" target="_blank"]] (advanced)
57 +* [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel="noopener noreferrer" target="_blank"]] (advanced)
58 +* [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel="noopener noreferrer" target="_blank"]] (advanced)
59 +* [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel="noopener noreferrer" target="_blank"]] (advanced)
60 +* [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel="noopener noreferrer" target="_blank"]] (advanced)
61 +* [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel="noopener noreferrer" target="_blank"]] (advanced)
62 +* [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel="noopener noreferrer" target="_blank"]] (advanced)
63 +* [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel="noopener noreferrer" target="_blank"]] (advanced)
64 +* [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel="noopener noreferrer" target="_blank"]] (advanced)
65 +* [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel="noopener noreferrer" target="_blank"]] (advanced)
66 +* [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel="noopener noreferrer" target="_blank"]] (advanced)
67 +* [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel="noopener noreferrer" target="_blank"]] (advanced)
68 +* [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel="noopener noreferrer" target="_blank"]] (advanced)
69 +* [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel="noopener noreferrer" target="_blank"]] (advanced)
70 +* [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel="noopener noreferrer" target="_blank"]] (advanced)
71 +* [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel="noopener noreferrer" target="_blank"]] (advanced)
72 +* [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel="noopener noreferrer" target="_blank"]] (advanced)
73 +* [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel="noopener noreferrer" target="_blank"]] (advanced)
74 +* [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel="noopener noreferrer" target="_blank"]] (advanced)
75 +* [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel="noopener noreferrer" target="_blank"]] (advanced)
76 +* [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel="noopener noreferrer" target="_blank"]] (advanced)
77 +* [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel="noopener noreferrer" target="_blank"]] (advanced)
78 +* [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel="noopener noreferrer" target="_blank"]] (advanced)
79 +* [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel="noopener noreferrer" target="_blank"]] (advanced)
80 +* [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel="noopener noreferrer" target="_blank"]] (advanced)
81 +* [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel="noopener noreferrer" target="_blank"]] (advanced)
82 +* [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel="noopener noreferrer" target="_blank"]] (advanced)
83 +* [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel="noopener noreferrer" target="_blank"]] (advanced)
84 +* [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel="noopener noreferrer" target="_blank"]] (advanced)
85 +* [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel="noopener noreferrer" target="_blank"]] (advanced)
86 +* [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel="noopener noreferrer" target="_blank"]] (advanced)
87 +* [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel="noopener noreferrer" target="_blank"]] (advanced)
88 +* [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel="noopener noreferrer" target="_blank"]] (advanced)
89 +* [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel="noopener noreferrer" target="_blank"]] (advanced)
62 62  
63 -=== **Miscellaneous** ===
91 +== Electrophysiology Analysis Toolkit ==
64 64  
65 -**[[EBRAINS Live Papers Viewer>>doc:.EBRAINS Live Papers Viewer.WebHome]]**
93 +* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] (beginner)
94 +* [[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)
95 +* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] (advanced)
96 +* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] (advanced)
97 +* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] (advanced)
98 +* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] (advanced)
99 +* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] (advanced)
66 66  
101 +== Hodgkin Huxley Neuron Builder ==
67 67  
68 -**Miscellaneous tutorials**
103 +* [[Hodgkin-Huxley Neuron Builder>>https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/web-resources-bsp/bsp-video-tutorials/HodgkinHuxleyNeuronBuilder/index.html||rel="noopener noreferrer" target="_blank"]] (advanced)
69 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
105 +== NEST ==
72 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
107 +* [[Introduction to NEST: Simulating a single neuron>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/videos/one_neuron.html||rel="noopener noreferrer" target="_blank"]] (beginner)
108 +* [[Neurons and simple neural networks>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_1_neurons_and_simple_neural_networks.html||rel="noopener noreferrer" target="_blank"]] (beginner)
109 +* [[Populations of neurons>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_2_populations_of_neurons.html||rel="noopener noreferrer" target="_blank"]] (beginner)
110 +* [[Connect two NEST simulations using MUSIC>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_2.html||rel="noopener noreferrer" target="_blank"]] (advanced)
111 +* [[Connecting networks with synapses>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.html||rel="noopener noreferrer" target="_blank"]] (advanced)
112 +* [[Introduction to the MUSIC Interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_1.html||rel="noopener noreferrer" target="_blank"]] (advanced)
113 +* [[MUSIC Connections in C++ and Python>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_3.html||rel="noopener noreferrer" target="_blank"]] (advanced)
114 +* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel="noopener noreferrer" target="_blank"]] (advanced)
115 +* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)
116 +* [[Spatially structured networks>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_4_spatially_structured_networks.html||rel="noopener noreferrer" target="_blank"]] (advanced)
117 +* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)
75 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
119 +== NESTML ==
78 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
121 +* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel="noopener noreferrer" target="_blank"]] (beginner)
122 +* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced)
123 +* [[Dopamine-modulated STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced)
124 +* [[Ornstein-Uhlenbeck noise tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced)
125 +* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced)
126 +* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel="noopener noreferrer" target="_blank"]] (advanced)
81 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
128 +== Neuron ==
84 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
130 +* [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel="noopener noreferrer" target="_blank"]] (beginner)
131 +* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel="noopener noreferrer" target="_blank"]] (beginner)
132 +* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel="noopener noreferrer" target="_blank"]] (advanced)
133 +* [[1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself-0||rel="noopener noreferrer" target="_blank"]] (advanced)
134 +* [[2. Run a "complete" simulation and save its results>>https://neuron.yale.edu/neuron/docs/2-run-complete-simulation-and-save-its-results||rel="noopener noreferrer" target="_blank"]] (advanced)
135 +* [[3. Run a segmented simulation and save its results>>https://neuron.yale.edu/neuron/docs/3-run-segmented-simulation-and-save-its-results||rel="noopener noreferrer" target="_blank"]] (advanced)
136 +* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel="noopener noreferrer" target="_blank"]] (advanced)
137 +* [[4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results||rel="noopener noreferrer" target="_blank"]] (advanced)
138 +* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel="noopener noreferrer" target="_blank"]] (advanced)
139 +* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel="noopener noreferrer" target="_blank"]] (advanced)
140 +* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel="noopener noreferrer" target="_blank"]] (advanced)
141 +* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel="noopener noreferrer" target="_blank"]] (advanced)
142 +* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel="noopener noreferrer" target="_blank"]] (advanced)
143 +* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel="noopener noreferrer" target="_blank"]] (advanced)
144 +* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel="noopener noreferrer" target="_blank"]] (advanced)
145 +* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel="noopener noreferrer" target="_blank"]] (advanced)
146 +* [[Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
147 +* [[Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
148 +* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
149 +* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
150 +* [[Dealing with simulations that generate a lot of data>>https://neuron.yale.edu/neuron/docs/dealing-simulations-generate-lot-data||rel="noopener noreferrer" target="_blank"]] (advanced)
151 +* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel="noopener noreferrer" target="_blank"]] (advanced)
152 +* [[Example: restricting a reaction to part of a region>>https://neuron.yale.edu/neuron/docs/example-restricting-reaction-part-region||rel="noopener noreferrer" target="_blank"]] (advanced)
153 +* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel="noopener noreferrer" target="_blank"]] (advanced)
154 +* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)
155 +* [[How to generate independent random spike streams>>https://neuron.yale.edu/neuron/docs/how-generate-independent-random-spike-streams||rel="noopener noreferrer" target="_blank"]] (advanced)
156 +* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
157 +* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel="noopener noreferrer" target="_blank"]] (advanced)
158 +* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel="noopener noreferrer" target="_blank"]] (advanced)
159 +* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel="noopener noreferrer" target="_blank"]] (advanced)
160 +* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel="noopener noreferrer" target="_blank"]] (advanced)
161 +* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)
162 +* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel="noopener noreferrer" target="_blank"]] (advanced)
163 +* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel="noopener noreferrer" target="_blank"]] (advanced)
164 +* [[Reaction-Diffusion: varying initial concentrations and parameters>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-varying-initial-concentrations-and-parameters||rel="noopener noreferrer" target="_blank"]] (advanced)
165 +* [[Reading a morphometric data file and converting it to a NEURON model>>https://neuron.yale.edu/neuron/docs/import3d/read_data||rel="noopener noreferrer" target="_blank"]] (advanced)
166 +* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel="noopener noreferrer" target="_blank"]] (advanced)
167 +* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel="noopener noreferrer" target="_blank"]] (advanced)
168 +* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel="noopener noreferrer" target="_blank"]] (advanced)
169 +* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel="noopener noreferrer" target="_blank"]] (advanced)
170 +* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel="noopener noreferrer" target="_blank"]] (advanced)
171 +* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
172 +* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel="noopener noreferrer" target="_blank"]] (advanced)
173 +* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
174 +* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
175 +* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
176 +* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)
177 +* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel="noopener noreferrer" target="_blank"]] (advanced)
178 +* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel="noopener noreferrer" target="_blank"]] (advanced)
87 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
180 +== Neurorobotics Platform ==
90 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
182 +* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel="noopener noreferrer" target="_blank"]] (beginner)
93 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
184 +== PyNN ==
96 96  
97 -**[[Innovation Funding Workshop>>https://youtu.be/JFxaoK2yMqI||rel=" noopener noreferrer" target="_blank"]]**
98 -**Level**: beginner(%%) **Type**: video tutorial
186 +* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] (beginner)
187 +* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] (beginner)
99 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
189 +== The Virtual Brain ==
102 102  
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**: -
191 +* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] (beginner)
192 +* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] (beginner)
193 +* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] (beginner)
194 +* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] (beginner)
195 +* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] (advanced)
196 +* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] (advanced)
197 +* [[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)
198 +* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)
199 +* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] (advanced)
200 +* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] (advanced)
201 +* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] (advanced)
202 +* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] (advanced)
203 +* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] (advanced)
204 +* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)
205 +* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] (advanced)
206 +* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)
207 +* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)
208 +* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)
209 +* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)
210 +* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)
211 +* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] (advanced)
212 +* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] (advanced)
213 +* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]] (advanced)
105 105  
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
215 +== VoluBA ==
108 108  
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
217 +* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] (-)
111 111  
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
219 +== ilastik ==
114 114  
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 -
221 +* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel="noopener noreferrer" target="_blank"]] (advanced)
222 +* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel="noopener noreferrer" target="_blank"]] (advanced)
223 +* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel="noopener noreferrer" target="_blank"]] (advanced)
224 +* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel="noopener noreferrer" target="_blank"]] (advanced)
225 +* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel="noopener noreferrer" target="_blank"]] (advanced)
226 +* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel="noopener noreferrer" target="_blank"]] (advanced)
227 +* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel="noopener noreferrer" target="_blank"]] (advanced)
228 +* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel="noopener noreferrer" target="_blank"]] (advanced)