Wiki source code of Arbor

Version 58.1 by abonard on 2025/05/23 13:15
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adavison 1.1 1
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abonard 3.1 3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
jessicamitchell 2.1 4
abonard 43.1 5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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abonard 3.1 7 === **Beginner** ===
jessicamitchell 2.1 8
abonard 3.1 9 === [[Arbor Tutorial Index – from Cells to Networks>>https://docs.arbor-sim.org/en/latest/tutorial/index.html||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 10
abonard 3.1 11 **Level**: beginner(%%) **Type**: interactive tutorial
jessicamitchell 2.1 12
abonard 42.1 13 === [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
jessicamitchell 2.1 14
abonard 42.1 15 **Level**: beginner(%%) **Type**: user documentation
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17 This tutorial will give you an intro into building a morphology from an arbor.segment_tree, region and locset expressions and into decors and cell decorations.
18 Furthermore will you learn about building an arbor.cable_cell object, arbor.single_cell_model object as well as running a simulation and visualising the results.
abonard 43.1 19 === **Advanced** ===
abonard 42.1 20
abonard 43.1 21 === [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] ===
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23 **Level**: advanced(%%) **Type**: user documentation
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25 This tutorial will show you how to build an arbor.context using a GPU. This requires that you have built Arbor with GPU support enabled. Further you will learn to build an arbor.domain_decomposition and provide an arbor.partition_hint. Finally you will profile an Arbor simulation using arbor.meter_manager.
abonard 44.1 26 === [[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"]] ===
abonard 43.1 27
abonard 44.1 28 **Level**: advanced(%%) **Type**: user documentation
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30 This tutorial will teach you how to take a model from the Allen Brain Atlas,
31 load a morphology from an swc file and a parameter fit file and apply it to an arbor.decor. It will further show you how to build an arbor.cable_cell representative of the cell in the model and an arbor.recipe reflective of the cell stimulation in the model. Finally you will be running a simulation and visualising these results.
abonard 45.1 32 === [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 44.1 33
abonard 45.1 34 **Level**: advanced(%%) **Type**: user documentation
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36 In this tutorial you will learn how to create a simulation recipe of a single dendrite. How to place probes on the morphology and running the simulation and extracting the results and finally investigate the influence of control volume policies.
abonard 46.1 37 === [[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"]] ===
abonard 45.1 38
abonard 46.1 39 **Level**: advanced(%%) **Type**: user documentation
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41 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.
abonard 47.1 42 === [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 46.1 43
abonard 47.1 44 **Level**: advanced(%%) **Type**: user documentation
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46 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.
abonard 48.1 47 === [[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"]] ===
abonard 47.1 48
abonard 48.1 49 **Level**: advanced(%%) **Type**: user documentation
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51 This tutorial will guide you through to create an ion channel with NMODL from scratch through a classic Hodgkin-Huxley ion channel model.
abonard 49.1 52 === [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 48.1 53
abonard 49.1 54 **Level**: advanced(%%) **Type**: user documentation
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56 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.
abonard 50.1 57 === [[Synapses in NMODL>>https://docs.arbor-sim.org/en/latest/tutorial/nmodl.html#synapses-in-nmodl||rel=" noopener noreferrer" target="_blank"]] ===
abonard 49.1 58
abonard 50.1 59 **Level**: advanced(%%) **Type**: user documentation
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61 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.
abonard 51.1 62 === [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 50.1 63
abonard 51.1 64 **Level**: advanced(%%) **Type**: user documentation
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66 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.
abonard 52.1 67 === [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 51.1 68
abonard 52.1 69 **Level**: advanced(%%) **Type**: user documentation
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71 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.
abonard 53.1 72 === [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 52.1 73
abonard 53.1 74 **Level**: advanced(%%) **Type**: user documentation
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76 This tutorial will teach you how to build an arbor.recipe., an arbor.context and
77 create an arbor.simulation. The running the simulation and visualising the results.
abonard 54.1 78 === [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 53.1 79
abonard 54.1 80 **Level**: advanced(%%) **Type**: user documentation
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82 We will focus on implementing a stochastic differential equation (SDE) in Arbor’s NMODL dialect and examine the mechanism code in the Arbor repository.
abonard 55.1 83 === [[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"]] ===
abonard 54.1 84
abonard 55.1 85 **Level**: advanced(%%) **Type**: user documentation
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87 You will be able to learn how to create a simulation recipe for two cells.
88 How to place probes, run the simulation and extract the results.
89 Finally you will able to add a gap junction connection.
abonard 56.1 90 === [[Brunel network>>https://docs.arbor-sim.org/en/latest/tutorial/brunel.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 55.1 91
abonard 56.1 92 **Level**: advanced(%%) **Type**: user documentation
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94 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.
abonard 57.1 95 === [[Optimisation of a Neocortical Layer 5 Pyramidal Cell in Arbor>>https://github.com/BlueBrain/BluePyOpt/blob/master/examples/l5pc/L5PC_arbor.ipynb||rel=" noopener noreferrer" target="_blank"]] ===
abonard 56.1 96
abonard 57.1 97 **Level**: advanced(%%) **Type**: interactive tutorial
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99 This notebook shows you how to optimise the maximal conductance of Neocortical Layer 5 Pyramidal Cell as used in Markram et al. 2015 using Arbor as the simulator.
abonard 58.1 100 === [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel=" noopener noreferrer" target="_blank"]] ===
abonard 57.1 101
abonard 58.1 102 **Level**: advanced(%%) **Type**: user documentation
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104 This tutorial will show you how to record transmembrane currents using arbor.cable_probe_total_current_cell and how to record stimulus currents using arbor.cable_probe_stimulus_current_cell. Later we will be using the arbor.place_pwlin API to map recorded transmembrane currents to extracellular potentials by deriving Arbor specific classes from LFPykit’s lfpykit.LineSourcePotential and lfpykit.CellGeometry.
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