Wiki source code of Arbor

Version 9.1 by abonard on 2025/04/10 15:02
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3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
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5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
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7 === **Beginner** ===
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9 === [[Arbor Tutorial Index – from Cells to Networks>>https://docs.arbor-sim.org/en/latest/tutorial/index.html||rel=" noopener noreferrer" target="_blank"]] ===
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11 **Level**: beginner(%%) **Type**: interactive tutorial
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13 === [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
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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.
19 === **Advanced** ===
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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.
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"]] ===
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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.
32 === [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" noopener noreferrer" target="_blank"]] ===
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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.
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"]] ===
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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.
42 === [[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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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.