Changes for page Tools and services tutorials
Last modified by abonard on 2025/05/23 13:23
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edited by abonard
on 2025/05/23 13:23
on 2025/05/23 13:23
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To version 16.1
edited by annedevismes
on 2023/02/22 14:42
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... ... @@ -1,133 +1,159 @@ 1 +(% style="text-align: center;" %) 2 +== **Findable. Accessible.** == 1 1 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 +(% class="wikigeneratedid" id="HWelcometothesingleentrypointtotutorialsforEBRAINStoolsandservices.Here2CyoucanfindalistofEBRAINSofferings2Csortedbytopic2Candlinkstotheirtutorials." style="text-align: center;" %) 5 +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. 7 7 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 +Some tutorials are also available on [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]]. 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 +== Arbor == 24 24 25 -=== **Medical Analytics** === 12 +* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner) 13 +* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] (advanced) 14 +* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced) 15 +* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] (advanced) 16 +* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] (advanced) 17 +* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced) 18 +* [[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) 19 +* [[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) 20 +* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] (advanced) 21 +* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] (advanced) 22 +* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] (advanced) 23 +* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced) 24 +* [[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) 26 26 27 -**[[Bids Manager & Pipeline>>doc:.Bids Manager & Pipeline.WebHome]]** 28 -**[[Brainstorm>>doc:.Brainstorm.WebHome]]** 26 +== Electrophysiology Analysis Toolkit == 29 29 30 -=== **Modelling and Simulation** === 28 +* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] (beginner) 29 +* [[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) 30 +* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] (advanced) 31 +* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] (advanced) 32 +* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] (advanced) 33 +* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] (advanced) 34 +* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] (advanced) 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]]** 36 +== NEST == 50 50 51 -=== **FAIR data** === 38 +* [[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) 39 +* [[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) 40 +* [[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) 41 +* [[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) 42 +* [[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) 43 +* [[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) 44 +* [[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) 45 +* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel="noopener noreferrer" target="_blank"]] (advanced) 46 +* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced) 47 +* [[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) 48 +* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel="noopener noreferrer" target="_blank"]] (advanced) 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]]** 50 +== NESTML == 58 58 59 -=== **Computing Infrastructure** === 52 +* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel="noopener noreferrer" target="_blank"]] (beginner) 53 +* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel="noopener noreferrer" target="_blank"]] (advanced) 54 +* [[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) 55 +* [[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) 56 +* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel="noopener noreferrer" target="_blank"]] (advanced) 57 +* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel="noopener noreferrer" target="_blank"]] (advanced) 60 60 61 - **[[SpiNNakerJupyter service>>doc:.SpiNNaker Jupyterservice.WebHome]]**59 +== Neuron == 62 62 63 -=== **Miscellaneous** === 61 +* [[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) 62 +* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel="noopener noreferrer" target="_blank"]] (beginner) 63 +* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel="noopener noreferrer" target="_blank"]] (advanced) 64 +* [[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) 65 +* [[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) 66 +* [[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) 67 +* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel="noopener noreferrer" target="_blank"]] (advanced) 68 +* [[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) 69 +* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel="noopener noreferrer" target="_blank"]] (advanced) 70 +* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel="noopener noreferrer" target="_blank"]] (advanced) 71 +* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel="noopener noreferrer" target="_blank"]] (advanced) 72 +* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel="noopener noreferrer" target="_blank"]] (advanced) 73 +* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel="noopener noreferrer" target="_blank"]] (advanced) 74 +* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel="noopener noreferrer" target="_blank"]] (advanced) 75 +* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel="noopener noreferrer" target="_blank"]] (advanced) 76 +* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel="noopener noreferrer" target="_blank"]] (advanced) 77 +* [[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) 78 +* [[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) 79 +* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 80 +* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 81 +* [[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) 82 +* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel="noopener noreferrer" target="_blank"]] (advanced) 83 +* [[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) 84 +* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel="noopener noreferrer" target="_blank"]] (advanced) 85 +* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced) 86 +* [[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) 87 +* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 88 +* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel="noopener noreferrer" target="_blank"]] (advanced) 89 +* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel="noopener noreferrer" target="_blank"]] (advanced) 90 +* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel="noopener noreferrer" target="_blank"]] (advanced) 91 +* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel="noopener noreferrer" target="_blank"]] (advanced) 92 +* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel="noopener noreferrer" target="_blank"]] (advanced) 93 +* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel="noopener noreferrer" target="_blank"]] (advanced) 94 +* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel="noopener noreferrer" target="_blank"]] (advanced) 95 +* [[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) 96 +* [[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) 97 +* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel="noopener noreferrer" target="_blank"]] (advanced) 98 +* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel="noopener noreferrer" target="_blank"]] (advanced) 99 +* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel="noopener noreferrer" target="_blank"]] (advanced) 100 +* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel="noopener noreferrer" target="_blank"]] (advanced) 101 +* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel="noopener noreferrer" target="_blank"]] (advanced) 102 +* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 103 +* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel="noopener noreferrer" target="_blank"]] (advanced) 104 +* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 105 +* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 106 +* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 107 +* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel="noopener noreferrer" target="_blank"]] (advanced) 108 +* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel="noopener noreferrer" target="_blank"]] (advanced) 109 +* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel="noopener noreferrer" target="_blank"]] (advanced) 64 64 65 - **[[EBRAINSLivePapers Viewer>>doc:.EBRAINSLivePapers Viewer.WebHome]]**111 +== Neurorobotics Platform == 66 66 113 +* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel="noopener noreferrer" target="_blank"]] (beginner) 67 67 68 - **Miscellaneoustutorials**115 +== PyNN == 69 69 70 -* *[[IPR, exploitation andtranslationof research- Lecture 7: Looking into the future using emergingtrends: What are they and howdo weidentify them? Part 1>>https://www.youtube.com/watch?v=8j6klXkSv0s&list=PLvAS8zldX4CjLAq5cpGG7cVtTC6n1lCtu&index=13||rel="**71 -* *Level**:beginner(%%)**Type**:videoresentation117 +* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] (beginner) 118 +* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] (beginner) 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 120 +== The Virtual Brain == 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 122 +* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] (beginner) 123 +* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] (beginner) 124 +* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] (beginner) 125 +* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] (beginner) 126 +* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] (advanced) 127 +* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] (advanced) 128 +* [[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) 129 +* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced) 130 +* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] (advanced) 131 +* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] (advanced) 132 +* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] (advanced) 133 +* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] (advanced) 134 +* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] (advanced) 135 +* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced) 136 +* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] (advanced) 137 +* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced) 138 +* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced) 139 +* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced) 140 +* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] (advanced) 141 +* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] (advanced) 142 +* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] (advanced) 143 +* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] (advanced) 144 +* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]] (advanced) 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 146 +== VoluBA == 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 148 +* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] (-) 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 150 +== ilastik == 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 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 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 96 - 97 -**[[Innovation Funding Workshop>>https://youtu.be/JFxaoK2yMqI||rel=" noopener noreferrer" target="_blank"]]** 98 -**Level**: beginner(%%) **Type**: video tutorial 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 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**: - 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 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 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 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 - 152 +* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel="noopener noreferrer" target="_blank"]] (advanced) 153 +* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel="noopener noreferrer" target="_blank"]] (advanced) 154 +* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel="noopener noreferrer" target="_blank"]] (advanced) 155 +* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel="noopener noreferrer" target="_blank"]] (advanced) 156 +* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel="noopener noreferrer" target="_blank"]] (advanced) 157 +* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel="noopener noreferrer" target="_blank"]] (advanced) 158 +* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel="noopener noreferrer" target="_blank"]] (advanced) 159 +* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel="noopener noreferrer" target="_blank"]] (advanced)