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1		-(% style="text-align: center;" %)
2		-=== 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. ===
3	3
	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		-This page is work in progress. It is incomplete for now. But it will include all of EBRAINS tutorials very soon.
	8	+Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
6	6
7		-Some tutorials are also available on [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
8	8
9		-== Arbor ==
	11	+=== Brain atlases ===
10	10
11		-* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] (beginner)
12		-* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
13		-* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
14		-* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
15		-* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
16		-* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
17		-* [[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)
18		-* [[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)
19		-* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
20		-* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
21		-* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
22		-* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
23		-* [[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)
	13	+|**[[VoluBA>>doc:.VoluBA.WebHome]]**
24	24
25		-== Bids Manager & Pipeline ==
26	26
27		-* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel=" noopener noreferrer" target="_blank"]] (advanced)
	16	+=== Data analysis ===
28	28
29		-== BluePyMM ==
	18	+|**[[Brainstorm>>doc:.Brainstorm.WebHome]]**
	19	+|**[[Electrophysiology Analysis Toolkit>>doc:.Electrophysiology Analysis Toolkit.WebHome]]**
	20	+|**[[ilastik>>doc:.ilastik.WebHome]]**
30	30
31		-* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel=" noopener noreferrer" target="_blank"]] (beginner)
32	32
33		-== BluePyOpt ==
	23	+=== Simulation ===
34	34
35		-* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel=" noopener noreferrer" target="_blank"]] (beginner)
	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]]**
36	36
37		-== Brainstorm ==
38	38
39		-* [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" noopener noreferrer" target="_blank"]] (beginner)
40		-* [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" noopener noreferrer" target="_blank"]] (advanced)
41		-* [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" noopener noreferrer" target="_blank"]] (advanced)
42		-* [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" noopener noreferrer" target="_blank"]] (advanced)
43		-* [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" noopener noreferrer" target="_blank"]] (advanced)
44		-* [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" noopener noreferrer" target="_blank"]] (advanced)
45		-* [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" noopener noreferrer" target="_blank"]] (advanced)
46		-* [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" noopener noreferrer" target="_blank"]] (advanced)
47		-* [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" noopener noreferrer" target="_blank"]] (advanced)
48		-* [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" noopener noreferrer" target="_blank"]] (advanced)
49		-* [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" noopener noreferrer" target="_blank"]] (advanced)
50		-* [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" noopener noreferrer" target="_blank"]] (advanced)
51		-* [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" noopener noreferrer" target="_blank"]] (advanced)
52		-* [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" noopener noreferrer" target="_blank"]] (advanced)
53		-* [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel=" noopener noreferrer" target="_blank"]] (advanced)
54		-* [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" noopener noreferrer" target="_blank"]] (advanced)
55		-* [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" noopener noreferrer" target="_blank"]] (advanced)
56		-* [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" noopener noreferrer" target="_blank"]] (advanced)
57		-* [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" noopener noreferrer" target="_blank"]] (advanced)
58		-* [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" noopener noreferrer" target="_blank"]] (advanced)
59		-* [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" noopener noreferrer" target="_blank"]] (advanced)
60		-* [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" noopener noreferrer" target="_blank"]] (advanced)
61		-* [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" noopener noreferrer" target="_blank"]] (advanced)
62		-* [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" noopener noreferrer" target="_blank"]] (advanced)
63		-* [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" noopener noreferrer" target="_blank"]] (advanced)
64		-* [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" noopener noreferrer" target="_blank"]] (advanced)
65		-* [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" noopener noreferrer" target="_blank"]] (advanced)
66		-* [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" noopener noreferrer" target="_blank"]] (advanced)
67		-* [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" noopener noreferrer" target="_blank"]] (advanced)
68		-* [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" noopener noreferrer" target="_blank"]] (advanced)
69		-* [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" noopener noreferrer" target="_blank"]] (advanced)
70		-* [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" noopener noreferrer" target="_blank"]] (advanced)
71		-* [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" noopener noreferrer" target="_blank"]] (advanced)
72		-* [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" noopener noreferrer" target="_blank"]] (advanced)
73		-* [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" noopener noreferrer" target="_blank"]] (advanced)
74		-* [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel=" noopener noreferrer" target="_blank"]] (advanced)
75		-* [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" noopener noreferrer" target="_blank"]] (advanced)
76		-* [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" noopener noreferrer" target="_blank"]] (advanced)
77		-* [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" noopener noreferrer" target="_blank"]] (advanced)
78		-* [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" noopener noreferrer" target="_blank"]] (advanced)
79		-* [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel=" noopener noreferrer" target="_blank"]] (advanced)
80		-* [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" noopener noreferrer" target="_blank"]] (advanced)
81		-* [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" noopener noreferrer" target="_blank"]] (advanced)
82		-* [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" noopener noreferrer" target="_blank"]] (advanced)
83		-* [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" noopener noreferrer" target="_blank"]] (advanced)
84		-* [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" noopener noreferrer" target="_blank"]] (advanced)
85		-* [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" noopener noreferrer" target="_blank"]] (advanced)
86		-* [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" noopener noreferrer" target="_blank"]] (advanced)
87		-* [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" noopener noreferrer" target="_blank"]] (advanced)
88		-* [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" noopener noreferrer" target="_blank"]] (advanced)
89		-* [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" noopener noreferrer" target="_blank"]] (advanced)
90		-* [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" noopener noreferrer" target="_blank"]] (advanced)
	36	+=== Neurorobotics ===
91	91
92		-== Electrophysiology Analysis Toolkit ==
	38	+|**[[Neurorobotics Platform>>doc:.Neurorobotics Platform.WebHome]]**
93	93
94		-* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel=" noopener noreferrer" target="_blank"]] (beginner)
95		-* [[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)
96		-* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
97		-* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
98		-* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
99		-* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
100		-* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
101	101
102		-== Hodgkin Huxley Neuron Builder ==
	41	+=== Medical data analytics ===
103	103
104		-* [[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)
	43	+|**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]**
105	105
106		-== NEST ==
107		-
108		-* [[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)
109		-* [[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)
110		-* [[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)
111		-* [[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)
112		-* [[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)
113		-* [[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)
114		-* [[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)
115		-* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
116		-* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
117		-* [[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)
118		-* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
119		-
120		-== NESTML ==
121		-
122		-* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel=" noopener noreferrer" target="_blank"]] (beginner)
123		-* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
124		-* [[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)
125		-* [[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)
126		-* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
127		-* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
128		-
129		-== Neuron ==
130		-
131		-* [[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)
132		-* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel=" noopener noreferrer" target="_blank"]] (beginner)
133		-* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
134		-* [[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)
135		-* [[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)
136		-* [[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)
137		-* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" noopener noreferrer" target="_blank"]] (advanced)
138		-* [[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)
139		-* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
140		-* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
141		-* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
142		-* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
143		-* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel=" noopener noreferrer" target="_blank"]] (advanced)
144		-* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" noopener noreferrer" target="_blank"]] (advanced)
145		-* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" noopener noreferrer" target="_blank"]] (advanced)
146		-* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" noopener noreferrer" target="_blank"]] (advanced)
147		-* [[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)
148		-* [[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)
149		-* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
150		-* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
151		-* [[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)
152		-* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" noopener noreferrer" target="_blank"]] (advanced)
153		-* [[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)
154		-* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" noopener noreferrer" target="_blank"]] (advanced)
155		-* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" noopener noreferrer" target="_blank"]] (advanced)
156		-* [[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)
157		-* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
158		-* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel=" noopener noreferrer" target="_blank"]] (advanced)
159		-* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
160		-* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" noopener noreferrer" target="_blank"]] (advanced)
161		-* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" noopener noreferrer" target="_blank"]] (advanced)
162		-* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" noopener noreferrer" target="_blank"]] (advanced)
163		-* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" noopener noreferrer" target="_blank"]] (advanced)
164		-* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" noopener noreferrer" target="_blank"]] (advanced)
165		-* [[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)
166		-* [[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)
167		-* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" noopener noreferrer" target="_blank"]] (advanced)
168		-* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" noopener noreferrer" target="_blank"]] (advanced)
169		-* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel=" noopener noreferrer" target="_blank"]] (advanced)
170		-* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" noopener noreferrer" target="_blank"]] (advanced)
171		-* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" noopener noreferrer" target="_blank"]] (advanced)
172		-* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
173		-* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel=" noopener noreferrer" target="_blank"]] (advanced)
174		-* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
175		-* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
176		-* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
177		-* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
178		-* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" noopener noreferrer" target="_blank"]] (advanced)
179		-* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel=" noopener noreferrer" target="_blank"]] (advanced)
180		-
181		-== Neurorobotics Platform ==
182		-
183		-* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel=" noopener noreferrer" target="_blank"]] (beginner)
184		-
185		-== PyNN ==
186		-
187		-* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel=" noopener noreferrer" target="_blank"]] (beginner)
188		-* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel=" noopener noreferrer" target="_blank"]] (beginner)
189		-
190		-== The Virtual Brain ==
191		-
192		-* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" noopener noreferrer" target="_blank"]] (beginner)
193		-* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" noopener noreferrer" target="_blank"]] (beginner)
194		-* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" noopener noreferrer" target="_blank"]] (beginner)
195		-* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" noopener noreferrer" target="_blank"]] (beginner)
196		-* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" noopener noreferrer" target="_blank"]] (advanced)
197		-* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" noopener noreferrer" target="_blank"]] (advanced)
198		-* [[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)
199		-* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
200		-* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" noopener noreferrer" target="_blank"]] (advanced)
201		-* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" noopener noreferrer" target="_blank"]] (advanced)
202		-* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" noopener noreferrer" target="_blank"]] (advanced)
203		-* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" noopener noreferrer" target="_blank"]] (advanced)
204		-* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" noopener noreferrer" target="_blank"]] (advanced)
205		-* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
206		-* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" noopener noreferrer" target="_blank"]] (advanced)
207		-* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
208		-* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
209		-* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] (advanced)
210		-* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel=" noopener noreferrer" target="_blank"]] (advanced)
211		-* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" noopener noreferrer" target="_blank"]] (advanced)
212		-* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" noopener noreferrer" target="_blank"]] (advanced)
213		-* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" noopener noreferrer" target="_blank"]] (advanced)
214		-* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" noopener noreferrer" target="_blank"]] (advanced)
215		-
216		-== VoluBA ==
217		-
218		-* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel=" noopener noreferrer" target="_blank"]] (-)
219		-
220		-== ilastik ==
221		-
222		-* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel=" noopener noreferrer" target="_blank"]] (advanced)
223		-* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel=" noopener noreferrer" target="_blank"]] (advanced)
224		-* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel=" noopener noreferrer" target="_blank"]] (advanced)
225		-* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel=" noopener noreferrer" target="_blank"]] (advanced)
226		-* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel=" noopener noreferrer" target="_blank"]] (advanced)
227		-* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel=" noopener noreferrer" target="_blank"]] (advanced)
228		-* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel=" noopener noreferrer" target="_blank"]] (advanced)
229		-* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel=" noopener noreferrer" target="_blank"]] (advanced)