Changes for page Tools and services tutorials
Last modified by abonard on 2025/05/23 13:23
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... ... @@ -1,62 +1,62 @@ 1 1 This page is in development. Once ready it will be moved to a public location. 2 2 3 -== Arbor == 3 +~== Arbor == 4 4 5 -* [[Arbor: A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] 6 -* [[Arbor: A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] 7 -* [[Arbor: A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] 8 -* [[Arbor: A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] 9 -* [[Arbor: A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] 10 -* [[Arbor: A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] 11 -* [[Arbor: 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"]] 12 -* [[Arbor: 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"]] 13 -* [[Arbor: Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] 14 -* [[Arbor: Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] 15 -* [[Arbor: GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] 16 -* [[Arbor: Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] 17 -* [[Arbor: 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"]] 5 +~* ~[~[Arbor: A detailed single cell model>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel="noopener noreferrer" target="_blank"]] 6 +~* ~[~[Arbor: A detailed single cell recipe>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel="noopener noreferrer" target="_blank"]] 7 +~* ~[~[Arbor: A ring network>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel="noopener noreferrer" target="_blank"]] 8 +~* ~[~[Arbor: A simple dendrite>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel="noopener noreferrer" target="_blank"]] 9 +~* ~[~[Arbor: A simple single cell model>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel="noopener noreferrer" target="_blank"]] 10 +~* ~[~[Arbor: A simple single cell recipe>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel="noopener noreferrer" target="_blank"]] 11 +~* ~[~[Arbor: 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"]] 12 +~* ~[~[Arbor: 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"]] 13 +~* ~[~[Arbor: Distributed ring network (MPI)>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel="noopener noreferrer" target="_blank"]] 14 +~* ~[~[Arbor: Extracellular signals (LFPykit)>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel="noopener noreferrer" target="_blank"]] 15 +~* ~[~[Arbor: GPU and profiling>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel="noopener noreferrer" target="_blank"]] 16 +~* ~[~[Arbor: Spike Timing-dependent Plasticity Curve>>https:~/~/docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel="noopener noreferrer" target="_blank"]] 17 +~* ~[~[Arbor: 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"]] 18 18 19 -== Electrophysiology Analysis Toolkit == 19 +~== Electrophysiology Analysis Toolkit == 20 20 21 -* [[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"]] 22 -* [[Gaussian Process Factor Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] 23 -* [[Parallel>>https://elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] 24 -* [[Spike Pattern Detection and Evaluation (SPADE)>>https://elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] 25 -* [[Statistics of spike trains>>https://elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] 26 -* [[The Unitary Events Analysis>>https://elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] 27 -* [[Time-domain Granger Causality>>https://elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] 21 +~* ~[~[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"]] 22 +~* ~[~[Gaussian Process Factor Analysis>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/gpfa.html||rel="noopener noreferrer" target="_blank"]] 23 +~* ~[~[Parallel>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/parallel.html||rel="noopener noreferrer" target="_blank"]] 24 +~* ~[~[Spike Pattern Detection and Evaluation (SPADE)>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/spade.html||rel="noopener noreferrer" target="_blank"]] 25 +~* ~[~[Statistics of spike trains>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/statistics.html||rel="noopener noreferrer" target="_blank"]] 26 +~* ~[~[The Unitary Events Analysis>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/unitary_event_analysis.html||rel="noopener noreferrer" target="_blank"]] 27 +~* ~[~[Time-domain Granger Causality>>https:~/~/elephant.readthedocs.io/en/latest/tutorials/granger_causality.html||rel="noopener noreferrer" target="_blank"]] 28 28 29 -== PyNN == 29 +~== PyNN == 30 30 31 -* [[Building and simulating a simple model>>https://youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] 32 -* [[Installing PyNN on a Linux system>>https://youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] 31 +~* ~[~[Building and simulating a simple model>>https:~/~/youtu.be/zBLNfJiEvRc||rel="noopener noreferrer" target="_blank"]] 32 +~* ~[~[Installing PyNN on a Linux system>>https:~/~/youtu.be/BZB7xKUK8Vc||rel="noopener noreferrer" target="_blank"]] 33 33 34 -== VoluBA == 34 +~== VoluBA == 35 35 36 -* [[Day 2 - 02. VoluBA (Sebastian Bludau)>>https://youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] 36 +~* ~[~[Day 2 - 02. VoluBA (Sebastian Bludau)>>https:~/~/youtu.be/l_7ILe6_2Cs||rel="noopener noreferrer" target="_blank"]] 37 37 38 -== The Virtual Brain == 38 +~== The Virtual Brain == 39 39 40 -* [[TVB: Brain stimulation in The Virtual Brain>>https://youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] 41 -* [[TVB: Building Your Own Brain Network Model>>https://docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] 42 -* [[TVB: Clinical Applications - Stroke Recovery & Dementia>>https://youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] 43 -* [[TVB: Evoked Responses in the Visual Cortex>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel="noopener noreferrer" target="_blank"]] 44 -* [[TVB: Exploring a model>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] 45 -* [[TVB: Getting Started>>https://docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] 46 -* [[TVB: Hands-On: Modeling stroke brain>>https://youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] 47 -* [[TVB: Human Brain Project (HBP) TVB-NEST co-simulation>>https://youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] 48 -* [[TVB: Import Virtual Brain ready data into TVB and create a brain model>>https://youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] 49 -* [[TVB: Integrated workflows: Image processing pipeline>>https://youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] 50 -* [[TVB: Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https://youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] 51 -* [[TVB: Modeling Epilepsy>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] 52 -* [[TVB: Modelling Epilepsy with The Virtual Brain>>https://youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] 53 -* [[TVB: My first simulation with The Virtual Brain>>https://youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] 54 -* [[TVB: Population Models in The Virtual Brain (TVB) and the Phase Plane>>https://youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] 55 -* [[TVB: Region simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] 56 -* [[TVB: Resting State Networks>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] 57 -* [[TVB: Simulating The Virtual Mouse Brain (TVMB)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] 58 -* [[TVB: Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https://youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] 59 -* [[TVB: Surface simulation tutorial>>https://nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] 60 -* [[TVB: Surface-based simulations and deep brain stimulations>>https://youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] 61 -* [[TVB: The Bayesian Virtual Epileptic Patient (BVEP)>>https://youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] 62 -* [[TVB: TVB to NEST multi-scale simulation>>https://youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]] 40 +~* ~[~[TVB: Brain stimulation in The Virtual Brain>>https:~/~/youtu.be/mskxBYKoeq0||rel="noopener noreferrer" target="_blank"]] 41 +~* ~[~[TVB: Building Your Own Brain Network Model>>https:~/~/docs.thevirtualbrain.org/tutorials/tutorial_1_BuildingYourOwnBrainNetworkModel.html#tutorial-1-buildingyourownbrainnetworkmodel||rel="noopener noreferrer" target="_blank"]] 42 +~* ~[~[TVB: Clinical Applications - Stroke Recovery & Dementia>>https:~/~/youtu.be/ZA2UuHZiPnM||rel="noopener noreferrer" target="_blank"]] 43 +~* ~[~[TVB: Evoked Responses in the Visual Cortex>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s4_EvokedResponsesInTheVisualCortex.ipynb||rel="noopener noreferrer" target="_blank"]] 44 +~* ~[~[TVB: Exploring a model>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s3_exploring_a_model.ipynb||rel="noopener noreferrer" target="_blank"]] 45 +~* ~[~[TVB: Getting Started>>https:~/~/docs.thevirtualbrain.org/tutorials/tutorial_0_GettingStarted.html#tutorial-0-gettingstarted||rel="noopener noreferrer" target="_blank"]] 46 +~* ~[~[TVB: Hands-On: Modeling stroke brain>>https:~/~/youtu.be/BDj9MLpt0io||rel="noopener noreferrer" target="_blank"]] 47 +~* ~[~[TVB: Human Brain Project (HBP) TVB-NEST co-simulation>>https:~/~/youtu.be/dUuQe_SI5lE||rel="noopener noreferrer" target="_blank"]] 48 +~* ~[~[TVB: Import Virtual Brain ready data into TVB and create a brain model>>https:~/~/youtu.be/OEOCFyiJgBM||rel="noopener noreferrer" target="_blank"]] 49 +~* ~[~[TVB: Integrated workflows: Image processing pipeline>>https:~/~/youtu.be/uUkq0K-xM0Q||rel="noopener noreferrer" target="_blank"]] 50 +~* ~[~[TVB: Modeling brain dynamics in brain tumor patients using The Virtual Brain>>https:~/~/youtu.be/t9xyoHxTAmQ||rel="noopener noreferrer" target="_blank"]] 51 +~* ~[~[TVB: Modeling Epilepsy>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s6_ModelingEpilepsy.ipynb||rel="noopener noreferrer" target="_blank"]] 52 +~* ~[~[TVB: Modelling Epilepsy with The Virtual Brain>>https:~/~/youtu.be/YrSxnMo6Lr8||rel="noopener noreferrer" target="_blank"]] 53 +~* ~[~[TVB: My first simulation with The Virtual Brain>>https:~/~/youtu.be/326iA14UVzY||rel="noopener noreferrer" target="_blank"]] 54 +~* ~[~[TVB: Population Models in The Virtual Brain (TVB) and the Phase Plane>>https:~/~/youtu.be/Zo0HGwLHN3E||rel="noopener noreferrer" target="_blank"]] 55 +~* ~[~[TVB: Region simulation tutorial>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s1_region_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] 56 +~* ~[~[TVB: Resting State Networks>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s5_ModelingRestingStateNetworks.ipynb||rel="noopener noreferrer" target="_blank"]] 57 +~* ~[~[TVB: Simulating The Virtual Mouse Brain (TVMB)>>https:~/~/youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] 58 +~* ~[~[TVB: Simulating The Virtual Mouse Brain (TVMB) (Copy)>>https:~/~/youtu.be/gxhJku8KRYY||rel="noopener noreferrer" target="_blank"]] 59 +~* ~[~[TVB: Surface simulation tutorial>>https:~/~/nbviewer.thevirtualbrain.org/url/docs.thevirtualbrain.org/tutorials/tutorial_s2_surface_simulation.ipynb||rel="noopener noreferrer" target="_blank"]] 60 +~* ~[~[TVB: Surface-based simulations and deep brain stimulations>>https:~/~/youtu.be/ZXLrvHc24xE||rel="noopener noreferrer" target="_blank"]] 61 +~* ~[~[TVB: The Bayesian Virtual Epileptic Patient (BVEP)>>https:~/~/youtu.be/4XghviA_1Uk||rel="noopener noreferrer" target="_blank"]] 62 +~* ~[~[TVB: TVB to NEST multi-scale simulation>>https:~/~/youtu.be/PppyGzWUxuE||rel="noopener noreferrer" target="_blank"]]