Wiki source code of Arbor

Version 102.1 by abonard on 2025/09/16 10:47
Show last authors
1
2
3 * ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
4
5 * ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
6
7 === **Beginner** ===
8
9 === [[Arbor Tutorial Index – from Cells to Networks>>https://docs.arbor-sim.org/en/latest/tutorial/index.html||rel=" noopener noreferrer" target="_blank"]] ===
10
11 **Level**: beginner(%%) **Type**: interactive tutorial
12
13 === [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
14
15 **Level**: beginner(%%) **Type**: user documentation
16
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** ===
20
21 === [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] ===
22
23 **Level**: advanced(%%) **Type**: user documentation
24
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"]] ===
27
28 **Level**: advanced(%%) **Type**: user documentation
29
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"]] ===
33
34 **Level**: advanced(%%) **Type**: user documentation
35
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.