Wiki source code of Tools and services tutorials

Version 19.1 by adavison on 2023/02/27 14:03

version	line-number	content
19.1	1	(% class="box infomessage" id="HWelcometothesingleentrypointtotutorialsforEBRAINStoolsandservices.Here2CyoucanfindalistofEBRAINSofferings2Csortedbytopic2Candlinkstotheirtutorials." style="text-align: center;" %)
	2	(((
	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.
	4	)))
8.1	5
19.1	6	Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].
12.1	7
3.1	8	== Arbor ==
1.1	9
19.1	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)
1.1	23
18.1	24	== Bids Manager & Pipeline ==
	25
19.1	26	* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf\|\|rel="noopener noreferrer" target="_blank"]] (advanced)
18.1	27
	28	== BluePyMM ==
	29
19.1	30	* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb\|\|rel="noopener noreferrer" target="_blank"]] (beginner)
18.1	31
	32	== BluePyOpt ==
	33
19.1	34	* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb\|\|rel="noopener noreferrer" target="_blank"]] (beginner)
18.1	35
	36	== Brainstorm ==
	37
19.1	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)
18.1	90
3.1	91	== Electrophysiology Analysis Toolkit ==
1.1	92
19.1	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)
1.1	100
18.1	101	== Hodgkin Huxley Neuron Builder ==
	102
19.1	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)
18.1	104
5.1	105	== NEST ==
	106
19.1	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)
5.1	118
6.1	119	== NESTML ==
	120
19.1	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)
6.1	127
	128	== Neuron ==
	129
19.1	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)
6.1	179
	180	== Neurorobotics Platform ==
	181
19.1	182	* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY\|\|rel="noopener noreferrer" target="_blank"]] (beginner)
6.1	183
3.1	184	== PyNN ==
1.1	185
19.1	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)
1.1	188
4.1	189	== The Virtual Brain ==
1.1	190
19.1	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)
1.1	214
4.1	215	== VoluBA ==
1.1	216
19.1	217	* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs\|\|rel="noopener noreferrer" target="_blank"]] (-)
6.1	218
	219	== ilastik ==
	220
19.1	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)

Wiki source code of Tools and services tutorials

EBRAINS Documentation