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... ... @@ -1,229 +1,228 @@ 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. === 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 +))) 3 3 6 +Some of the tutorials can also be accessed via the [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]]. 4 4 5 -This page is work in progress. It is incomplete for now. But it will include all of EBRAINS tutorials very soon. 6 - 7 -Some tutorials are also available on [[EBRAINS YouTube channel>>https://www.youtube.com/channel/UC6E796cVVR5Xrs2A5jJmleQ]]. 8 - 9 9 == Arbor == 10 10 11 -* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" 12 -* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" 13 -* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" 14 -* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" 15 -* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" 16 -* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" 17 -* [[A single cell model from the Allen Brain Atlas>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_allen.html||rel=" 18 -* [[A single cell model from the BluePyOpt Cell Optimisation Library>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_bluepyopt.html||rel=" 19 -* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" 20 -* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel=" 21 -* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" 22 -* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" 23 -* [[Two cells connected via a gap junction>>https://docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel=" 10 +* [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] (beginner) 11 +* [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] (advanced) 12 +* [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced) 13 +* [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] (advanced) 14 +* [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] (advanced) 15 +* [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] (advanced) 16 +* [[A single cell model from the Allen Brain Atlas>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_allen.html||rel="noopener noreferrer" target="_blank"]] (advanced) 17 +* [[A single cell model from the BluePyOpt Cell Optimisation Library>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_bluepyopt.html||rel="noopener noreferrer" target="_blank"]] (advanced) 18 +* [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] (advanced) 19 +* [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] (advanced) 20 +* [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] (advanced) 21 +* [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] (advanced) 22 +* [[Two cells connected via a gap junction>>https://docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel="noopener noreferrer" target="_blank"]] (advanced) 24 24 25 25 == Bids Manager & Pipeline == 26 26 27 -* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel=" 26 +* [[BIDS Manager>>https://github.com/Dynamap/BIDS_Manager/blob/master/Tutorial_BIDS_Manager.pdf||rel="noopener noreferrer" target="_blank"]] (advanced) 28 28 29 29 == BluePyMM == 30 30 31 -* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel=" 30 +* [[BluePyMM>>https://github.com/BlueBrain/BluePyMM/blob/master/notebook/BluePyMM.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner) 32 32 33 33 == BluePyOpt == 34 34 35 -* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel=" 34 +* [[Creating a simple cell optimisation>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/simplecell/simplecell.ipynb||rel="noopener noreferrer" target="_blank"]] (beginner) 36 36 37 37 == Brainstorm == 38 38 39 -* [[Introduction tutorials>>https://neuroimage.usc.edu/brainstorm/Tutorials/AllIntroduction||rel=" 40 -* [[Best: Brain Entropy in space and time>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutBEst||rel=" 41 -* [[Connectivity>>https://neuroimage.usc.edu/brainstorm/Tutorials/Connectivity||rel=" 42 -* [[Connectivity Graphs>>https://neuroimage.usc.edu/brainstorm/Tutorials/ConnectivityGraph||rel=" 43 -* [[Converting to Brainstorm Events>>https://neuroimage.usc.edu/brainstorm/e-phys/ConvertToBrainstormEvents||rel=" 44 -* [[Coordinate systems>>https://neuroimage.usc.edu/brainstorm/CoordinateSystems||rel=" 45 -* [[Corticomuscular coherence (CTF MEG)>>https://neuroimage.usc.edu/brainstorm/Tutorials/CorticomuscularCoherence||rel=" 46 -* [[Deriving LFP signals from raw signals>>https://neuroimage.usc.edu/brainstorm/e-phys/RawToLFP||rel=" 47 -* [[Digitize EEG sensor locations and head shape>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutDigitize||rel=" 48 -* [[ECoG/sEEG tutorial>>https://neuroimage.usc.edu/brainstorm/Tutorials/ECoG||rel=" 49 -* [[EEG and epilepsy>>https://neuroimage.usc.edu/brainstorm/Tutorials/Epilepsy||rel=" 50 -* [[Elekta-Neuromag tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutMindNeuromag||rel=" 51 -* [[Epileptogenic Zone Fingerprint>>https://neuroimage.usc.edu/brainstorm/Tutorials/EZFingerprint||rel=" 52 -* [[Export raw files in BIDS format>>https://neuroimage.usc.edu/brainstorm/ExportBids||rel=" 53 -* [[Export surface source maps to SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm12||rel=" 54 -* [[Export volume source maps to SPM8 / SPM12>>https://neuroimage.usc.edu/brainstorm/ExportSpm8||rel=" 55 -* [[FEM advanced tutorial with MEG/EEG Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMedianNerve||rel=" 56 -* [[FEM mesh generation>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemMesh||rel=" 57 -* [[FEM tensors estimation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/FemTensors||rel=" 58 -* [[Fitting dipoles with FieldTrip>>https://neuroimage.usc.edu/brainstorm/Tutorials/DipoleFitting||rel=" 59 -* [[Fitting Oscillations and One-Over-F (FOOOF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/Fooof||rel=" 60 -* [[Functions for Basic e-phys>>https://neuroimage.usc.edu/brainstorm/e-phys/functions||rel=" 61 -* [[Granger causality>>https://neuroimage.usc.edu/brainstorm/GrangerCausality||rel=" 62 -* [[Group analysis: Subject coregistration>>https://neuroimage.usc.edu/brainstorm/Tutorials/CoregisterSubjects||rel=" 63 -* [[How to write your own process>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutUserProcess||rel=" 64 -* [[Human Connectome Project: Resting-state MEG>>https://neuroimage.usc.edu/brainstorm/Tutorials/HCP-MEG||rel=" 65 -* [[MEG current phantom (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomCtf||rel=" 66 -* [[MEG current phantom (Elekta-Neuromag)>>https://neuroimage.usc.edu/brainstorm/Tutorials/PhantomElekta||rel=" 67 -* [[MEG median nerve tutorial (CTF)>>https://neuroimage.usc.edu/brainstorm/Tutorials/MedianNerveCtf||rel=" 68 -* [[MEG visual tutorial: Group analysis (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualGroup||rel=" 69 -* [[MEG visual tutorial: Single subject (BIDS)>>https://neuroimage.usc.edu/brainstorm/Tutorials/VisualSingle||rel=" 70 -* [[Montage editor>>https://neuroimage.usc.edu/brainstorm/Tutorials/MontageEditor||rel=" 71 -* [[MRI Segmentation with CAT12>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCAT12||rel=" 72 -* [[MRI segmentation with CIVET>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegCIVET||rel=" 73 -* [[MRI segmentation with FastSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegFastSurfer||rel=" 74 -* [[NIRS data importation, visualization and response estimate in the optode space>>https://neuroimage.usc.edu/brainstorm/Tutorials/NIRSFingerTapping||rel=" 75 -* [[Plugins>>https://neuroimage.usc.edu/brainstorm/Tutorials/Plugins||rel=" 76 -* [[Real-time head-tracking for adjusting head position>>https://neuroimage.usc.edu/brainstorm/Tutorials/TutRealtime||rel=" 77 -* [[Realistic head model: FEM with DUNEuro>>https://neuroimage.usc.edu/brainstorm/Tutorials/Duneuro||rel=" 78 -* [[Resting state recordings from the OMEGA database>>https://neuroimage.usc.edu/brainstorm/Tutorials/RestingOmega||rel=" 79 -* [[Simulations>>https://neuroimage.usc.edu/brainstorm/Tutorials/Simulations||rel=" 80 -* [[Spectral Parameterization Resolved in Time (SPRiNT)>>https://neuroimage.usc.edu/brainstorm/Tutorials/SPRiNT||rel=" 81 -* [[Spike Sorting in Brainstorm>>https://neuroimage.usc.edu/brainstorm/e-phys/SpikeSorting||rel=" 82 -* [[SSP Cookbook>>https://neuroimage.usc.edu/brainstorm/Tutorials/SSPCookbook||rel=" 83 -* [[Synchronization with eye tracker (event transfer)>>https://neuroimage.usc.edu/brainstorm/Tutorials/EyetrackSynchro||rel=" 84 -* [[T1-MRI Segmentation with BrainSuite>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainSuite||rel=" 85 -* [[Tutorial - Head Motion>>https://neuroimage.usc.edu/brainstorm/Tutorials/HeadMotion||rel=" 86 -* [[Using BrainVISA>>https://neuroimage.usc.edu/brainstorm/Tutorials/SegBrainVisa||rel=" 87 -* [[Using FreeSurfer>>https://neuroimage.usc.edu/brainstorm/Tutorials/LabelFreeSurfer||rel=" 88 -* [[Using the anatomy templates>>https://neuroimage.usc.edu/brainstorm/Tutorials/DefaultAnatomy||rel=" 89 -* [[Virtual Fiber Tracks for Connectivity Visualization>>https://neuroimage.usc.edu/brainstorm/Tutorials/FiberConnectivity||rel=" 90 -* [[Yokogawa/KIT tutorial: Median nerve stimulation>>https://neuroimage.usc.edu/brainstorm/Tutorials/Yokogawa||rel=" 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) 91 91 92 92 == Electrophysiology Analysis Toolkit == 93 93 94 -* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel=" 95 -* [[ASSET: Analysis of Sequences of Synchronous Events in Massively Parallel Spike Trains>>https://elephant.readthedocs.io/en/latest/tutorials/asset.html||rel=" 96 -* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel=" 97 -* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel=" 98 -* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel=" 99 -* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel=" 100 -* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel=" 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) 101 101 102 102 == Hodgkin Huxley Neuron Builder == 103 103 104 -* [[Hodgkin-Huxley Neuron Builder>>https://object.cscs.ch/v1/AUTH_c0a333ecf7c045809321ce9d9ecdfdea/web-resources-bsp/bsp-video-tutorials/HodgkinHuxleyNeuronBuilder/index.html||rel=" 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) 105 105 106 106 == NEST == 107 107 108 -* [[Introduction to NEST: Simulating a single neuron>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/videos/one_neuron.html||rel=" 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=" 110 -* [[Populations of neurons>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_2_populations_of_neurons.html||rel=" 111 -* [[Connect two NEST simulations using MUSIC>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_2.html||rel=" 112 -* [[Connecting networks with synapses>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_3_connecting_networks_with_synapses.html||rel=" 113 -* [[Introduction to the MUSIC Interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_1.html||rel=" 114 -* [[MUSIC Connections in C++ and Python>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_3.html||rel=" 115 -* [[MUSIC with SLI>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_sli.html||rel=" 116 -* [[Practical tips>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel=" 117 -* [[Spatially structured networks>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/pynest_tutorial/part_4_spatially_structured_networks.html||rel=" 118 -* [[The pymusic interface>>https://nest-simulator.readthedocs.io/en/v3.3/tutorials/music_tutorial/music_tutorial_4.html||rel=" 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) 119 119 120 120 == NESTML == 121 121 122 -* [[Izhikevich tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/izhikevich/nestml_izhikevich_tutorial.html||rel=" 123 -* [[Active dendrite tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/active_dendrite/nestml_active_dendrite_tutorial.html||rel=" 124 -* [[Dopamine-modulated STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_dopa_synapse/stdp_dopa_synapse.html||rel=" 125 -* [[Ornstein-Uhlenbeck noise tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/ornstein_uhlenbeck_noise/nestml_ou_noise_tutorial.html||rel=" 126 -* [[STDP synapse tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/triplet_stdp_synapse/triplet_stdp_synapse.html||rel=" 127 -* [[STDP windows tutorial>>https://nestml.readthedocs.io/en/latest/tutorials/stdp_windows/stdp_windows.html||rel=" 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) 128 128 129 129 == Neuron == 130 130 131 -* [[Construction and Use of Models: Part 1. Elementary tools>>https://neuron.yale.edu/neuron/static/docs/elementarytools/outline.htm||rel=" 132 -* [[The hoc programming language>>https://neuron.yale.edu/neuron/static/docs/programming/hoc_slides.pdf||rel=" 133 -* [[ Introduction to Network Construction>>https://neuron.yale.edu/neuron/static/docs/netbuild/intro.html||rel=" 134 -* [[1. Implement and test the computational model itself>>https://neuron.yale.edu/neuron/docs/1-implement-and-test-computational-model-itself-0||rel=" 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=" 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=" 137 -* [[3D/Hybrid Intracellular Tutorial>>https://neuron.yale.edu/neuron/docs/3dhybrid-intracellular-tutorial||rel=" 138 -* [[4. Reconstitute and verify the "complete" simulation results>>https://neuron.yale.edu/neuron/docs/4-reconstitute-and-verify-complete-simulation-results||rel=" 139 -* [[A NEURON Programming Tutorial - Part A>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutA.html||rel=" 140 -* [[A NEURON Programming Tutorial - Part B>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutB.html||rel=" 141 -* [[A NEURON Programming Tutorial - part C>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutC.html||rel=" 142 -* [[A NEURON Programming Tutorial - Part E>>http://web.mit.edu/neuron_v7.4/nrntuthtml/tutorial/tutE.html||rel=" 143 -* [[Ball and Stick model part 1>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-1||rel=" 144 -* [[Ball and Stick model part 2>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-2||rel=" 145 -* [[Ball and Stick model part 3>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-3||rel=" 146 -* [[Ball and Stick model part 4>>https://neuron.yale.edu/neuron/docs/ball-and-stick-model-part-4||rel=" 147 -* [[Creating a channel from a kinetic scheme specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/kinetic/outline.html||rel=" 148 -* [[Creating a channel from an HH-style specification>>https://neuron.yale.edu/neuron/static/docs/chanlbild/hhstyle/outline.html||rel=" 149 -* [[Creating a model of stochastic channel gating>>https://neuron.yale.edu/neuron/static/docs/chanlbild/stochastic/outline.html||rel=" 150 -* [[Creating a stylized ("stick figure") model cell>>https://neuron.yale.edu/neuron/static/docs/cbtut/stylized/outline.html||rel=" 151 -* [[Dealing with simulations that generate a lot of data>>https://neuron.yale.edu/neuron/docs/dealing-simulations-generate-lot-data||rel=" 152 -* [[Example: circadian rhythm>>https://neuron.yale.edu/neuron/docs/example-circadian-rhythm||rel=" 153 -* [[Example: restricting a reaction to part of a region>>https://neuron.yale.edu/neuron/docs/example-restricting-reaction-part-region||rel=" 154 -* [[Exploring morphometric data and fixing problems>>https://neuron.yale.edu/neuron/docs/import3d/fix_problems||rel=" 155 -* [[Extracellular Diffusion>>https://neuron.yale.edu/neuron/docs/extracellular-diffusion||rel=" 156 -* [[How to generate independent random spike streams>>https://neuron.yale.edu/neuron/docs/how-generate-independent-random-spike-streams||rel=" 157 -* [[Managing a model cell with complex anatomy>>https://neuron.yale.edu/neuron/static/docs/cbtut/pt3d/outline.html||rel=" 158 -* [[mGluR example>>https://neuron.yale.edu/neuron/docs/mglur-example||rel=" 159 -* [[ModelView: Compact display of parameters for NEURON models.>>https://neuron.yale.edu/neuron/static/papers/mview/modelviewhbp2004.html||rel=" 160 -* [[Python introduction>>https://neuron.yale.edu/neuron/docs/python-introduction||rel=" 161 -* [[Randomness in NEURON models>>https://neuron.yale.edu/neuron/docs/randomness-neuron-models||rel=" 162 -* [[Reaction-Diffusion>>https://neuron.yale.edu/neuron/docs/reaction-diffusion||rel=" 163 -* [[Reaction-Diffusion: Calcium Wave>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-calcium-wave||rel=" 164 -* [[Reaction-Diffusion: Thresholds>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-thresholds||rel=" 165 -* [[Reaction-Diffusion: varying initial concentrations and parameters>>https://neuron.yale.edu/neuron/docs/reaction-diffusion-varying-initial-concentrations-and-parameters||rel=" 166 -* [[Reading a morphometric data file and converting it to a NEURON model>>https://neuron.yale.edu/neuron/docs/import3d/read_data||rel=" 167 -* [[RxD with MOD files>>https://neuron.yale.edu/neuron/docs/rxd-mod-files||rel=" 168 -* [[Scripting NEURON basics>>https://neuron.yale.edu/neuron/docs/scripting-neuron-basics||rel=" 169 -* [[Segmenting a simulation of a model cell>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-cell||rel=" 170 -* [[Segmenting a simulation of a model network>>https://neuron.yale.edu/neuron/docs/segmenting-simulation-model-network||rel=" 171 -* [[Source code that demonstrates the solution>>https://neuron.yale.edu/neuron/docs/source-code-demonstrates-solution||rel=" 172 -* [[Specifying parameterized variation of biophysical properties>>https://neuron.yale.edu/neuron/static/docs/cbtut/parameterized/outline.html||rel=" 173 -* [[The solution>>https://neuron.yale.edu/neuron/docs/solution||rel=" 174 -* [[Tutorial 1 : Fitting a function to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/func/outline.html||rel=" 175 -* [[Tutorial 1: Making Networks of Artificial Neurons>>https://neuron.yale.edu/neuron/static/docs/netbuild/artnet/outline.html||rel=" 176 -* [[Tutorial 2 : Fitting a model to data>>https://neuron.yale.edu/neuron/static/docs/optimiz/model/outline.html||rel=" 177 -* [[Tutorial 2: Making Hybrid Nets>>https://neuron.yale.edu/neuron/static/docs/netbuild/hybrid/outline.html||rel=" 178 -* [[Using Import3D>>https://neuron.yale.edu/neuron/docs/import3d||rel=" 179 -* [[Using NEURON's Optimization Tools>>https://neuron.yale.edu/neuron/static/docs/optimiz/main.html||rel=" 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) 180 180 181 181 == Neurorobotics Platform == 182 182 183 -* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel=" 182 +* [[Drag and drop experiment set up with multiple robots>>https://youtu.be/VF3xd3mXTqY||rel="noopener noreferrer" target="_blank"]] (beginner) 184 184 185 185 == PyNN == 186 186 187 -* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel=" 188 -* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel=" 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) 189 189 190 190 == The Virtual Brain == 191 191 192 -* [[Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel=" 193 -* [[Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel=" 194 -* [[My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel=" 195 -* [[Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel=" 196 -* [[Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel=" 197 -* [[Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel=" 198 -* [[Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel=" 199 -* [[Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel=" 200 -* [[Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel=" 201 -* [[Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel=" 202 -* [[Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel=" 203 -* [[Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel=" 204 -* [[Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel=" 205 -* [[Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel=" 206 -* [[Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel=" 207 -* [[Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel=" 208 -* [[Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel=" 209 -* [[Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel=" 210 -* [[Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel=" 211 -* [[Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel=" 212 -* [[Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel=" 213 -* [[The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel=" 214 -* [[TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel=" 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) 215 215 216 216 == VoluBA == 217 217 218 -* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel=" 217 +* [[Anchoring partial volumetric data to BigBrain using VoluBA>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] (-) 219 219 220 220 == ilastik == 221 221 222 -* [[Boundary-based segmentation with Multicut>>https://youtu.be/leuTtIAmEwE||rel=" 223 -* [[Carving Workflow>>https://youtu.be/xGyTriPQXHI||rel=" 224 -* [[Cell Density Counting Workflow>>https://youtu.be/N-QhiTWVDmk||rel=" 225 -* [[EBRAINS Atlases - QUINT workflow Tutorial>>https://youtu.be/n-gQigcGMJ0||rel=" 226 -* [[Object Classification>>https://youtu.be/SQeRGvHeT3o||rel=" 227 -* [[Pixel Classification workflow>>https://youtu.be/5N0XYW9gRZY||rel=" 228 -* [[Tracking MaMuT Export>>https://youtu.be/kjVqWSSdDmU||rel=" 229 -* [[Tracking workflow>>https://youtu.be/bZoWx2FuT08||rel=" 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)