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**Level**: advanced(%%) **Type**: user documentation |
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Export a model with optimised parameters from BluePyOpt to a mixed JSON/ACC format. Load the morphology, label dictionary and decor from the mixed JSON/ACC format in Arbor. Perform axon replacement with a surrogate model using the segment tree editing functionality. Determine voltage probe locations that match BluePyOpt protocols defined with the Neuron simulator using the Arbor graphical user interface (GUI). Create an arbor.cable_cell and an arbor.single_cell_model or arbor.recipe supporting mechanism catalogues that are consistent with BluePyOpt. Running a simulation and visualising the results. |
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-=== [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-In this tutorial you will learn how to build an arbor.recipe and using this recipe, default context and domain decomposition to create an arbor.simulation. Running the simulation and visualizing the results. |
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-=== [[How to use NMODL to extend Arbor’s repertoire of Ion Channels>>https://docs.arbor-sim.org/en/latest/tutorial/nmodl.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-This tutorial will guide you through to create an ion channel with NMODL from scratch through a classic Hodgkin-Huxley ion channel model. |
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-=== [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-In this tutorial you will learn how to build a morphology from an arbor.segment_tree. Building a morphology from an SWC file. Writing and visualizing region and locset expressions. Building a decor and discretising the morphology. Setting and overriding model and cell parameters. Running a simulation and visualising the results using a arbor.single_cell_model. |
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-=== [[Synapses in NMODL>>https://docs.arbor-sim.org/en/latest/tutorial/nmodl.html#synapses-in-nmodl||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-This tutorial will show and discuss the exponential synapse coming with Arbor. This tutorial builds on "How to use NMODL to extend Arbor’s repertoire of Ion Channels", so please make sure you are familiar with it before going over this tutorial. |
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-=== [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-This tutorial teaches you how to build a basic arbor.cell with a synapse site and spike generator, as well as build an arbor.recipe with a network of interconnected cells. Finally you will be able to run the simulation and extract the results. |
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-=== [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-This tutorials will teach you how to build a basic MPI aware arbor.context to run a network. This requires that you have built Arbor with MPI support enabled. Finally you will run the simulation and extract the results. |
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-=== [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-This tutorial will teach you how to build an arbor.recipe., an arbor.context and |
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-create an arbor.simulation. The running the simulation and visualising the results. |
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-=== [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-We will focus on implementing a stochastic differential equation (SDE) in Arbor’s NMODL dialect and examine the mechanism code in the Arbor repository. |
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-=== [[Two cells connected via a gap junction>>https://docs.arbor-sim.org/en/stable/tutorial/network_two_cells_gap_junctions.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-You will be able to learn how to create a simulation recipe for two cells. |
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-How to place probes, run the simulation and extract the results. |
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-Finally you will able to add a gap junction connection. |
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-=== [[Brunel network>>https://docs.arbor-sim.org/en/latest/tutorial/brunel.html||rel=" noopener noreferrer" target="_blank"]] === |
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-**Level**: advanced(%%) **Type**: user documentation |
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-In this tutorial we will follow the description of the ring network to build our recipe. Finally you will be able to build the network, run the simulation, and record the spikes. If interested you can go on to learn how to visualise the raster plot of the entire network and a few selected cells, and the peristimulus time histogram (PSTH) of the entire network. |
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