Tools and services tutorials

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== **Findable. Accessible. User-facing.** ==

=== 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. ===

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Some tutorials are also available on [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]].

== Arbor ==

* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[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)

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* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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== Electrophysiology Analysis Toolkit ==

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* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[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)

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* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== NEST ==

* [[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)

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* [[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)

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* [[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)

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* [[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)

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* [[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)

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* [[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)

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* [[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)

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* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== NESTML ==

* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[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)

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* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel="noopener noreferrer" target="_blank"]] (advanced)

== Neuron ==

* [[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)

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* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[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)

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* [[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)

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* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[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)

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* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[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)

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* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel="noopener noreferrer" target="_blank"]] (advanced)

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== Neurorobotics Platform ==

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* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel="noopener noreferrer" target="_blank"]] (beginner)

== PyNN ==

* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] (beginner)

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== The Virtual Brain ==

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* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] (beginner)

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* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[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)

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* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]] (advanced)

== VoluBA ==

* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] (-)

== ilastik ==

* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel="noopener noreferrer" target="_blank"]] (advanced)

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* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel="noopener noreferrer" target="_blank"]] (advanced)

Wiki source code of Tools and services tutorials

EBRAINS Documentation