Wiki source code of Arbor

Version 7.1 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.