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1		-XWiki.jessicamitchell
	1	+XWiki.abonard

Content

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1		-Available tutorials:
2	2
3		-=== [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
4	4
5		-//Level: beginner//
	3	+* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
6	6
7		-Intro to building a morphology from a arbor.segment_tree.
8		-Intro to region and locset expressions.
9		-Intro to decors and cell decorations.
10		-Building a arbor.cable_cell object.
11		-Building a arbor.single_cell_model object.
12		-Running a simulation and visualising the results.
13		-=== [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] ===
	5	+* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
14	14
15		-//Level: advanced//
	7	+=== **Beginner** ===
16	16
17		-Building a morphology from a arbor.segment_tree.
18		-Building a morphology from an SWC file.
19		-Writing and visualizing region and locset expressions.
20		-Building a decor.
21		-Discretising the morphology.
22		-Setting and overriding model and cell parameters.
23		-Running a simulation and visualising the results using a arbor.single_cell_model.
24		-=== [[A detailed single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed_recipe.html||rel=" noopener noreferrer" target="_blank"]] ===
	9	+=== [[Arbor Tutorial Index – from Cells to Networks>>https://docs.arbor-sim.org/en/latest/tutorial/index.html||rel=" noopener noreferrer" target="_blank"]] ===
25	25
26		-//Level: advanced//
	11	+**Level**: beginner(%%) **Type**: interactive tutorial
27	27
28		-Building a arbor.recipe.
29		-Building an arbor.context.
30		-Create a arbor.simulation.
31		-Running the simulation and visualizing the results.
32		-=== [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] ===
	13	+=== [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
33	33
34		-//Level: advanced//
	15	+**Level**: beginner(%%) **Type**: user documentation
35	35
36		-Building a basic arbor.cell with a synapse site and spike generator.
37		-Building a arbor.recipe with a network of interconnected cells.
38		-Running the simulation and extract the results.
39		-=== [[A simple dendrite>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_cable.html||rel=" noopener noreferrer" target="_blank"]] ===
	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** ===
40	40
41		-//Level: advanced//
	21	+=== [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] ===
42	42
43		-Creating a simulation recipe of a single dendrite.
44		-Placing probes on the morphology.
45		-Running the simulation and extracting the results.
46		-Investigating the influence of control volume policies.
47		-=== [[A simple single cell recipe>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_recipe.html||rel=" noopener noreferrer" target="_blank"]] ===
	23	+**Level**: advanced(%%) **Type**: user documentation
48	48
49		-//Level: advanced//
50		-
51		-Building a arbor.recipe.
52		-Using the recipe, default context and domain decomposition to create an arbor.simulation
53		-Running the simulation and visualizing the results.
	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.
54	54	=== [[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"]] ===
55	55
56		-//Level: advanced//
	28	+**Level**: advanced(%%) **Type**: user documentation
57	57
58		-Take a model from the Allen Brain Atlas.
59		-Load a morphology from an swc file.
60		-Load a parameter fit file and apply it to a arbor.decor.
61		-Building a arbor.cable_cell representative of the cell in the model.
62		-Building a arbor.recipe reflective of the cell stimulation in the model.
63		-Running a simulation and visualising the results.
64		-=== [[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"]] ===
	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"]] ===
65	65
66		-//Level: advanced//
	34	+**Level**: advanced(%%) **Type**: user documentation
67	67
68		-Export a model with optimised parameters from BluePyOpt to a mixed JSON/ACC format.
69		-Load the morphology, label dictionary and decor from the mixed JSON/ACC format in Arbor.
70		-Perform axon replacement with a surrogate model using the segment tree editing functionality.
71		-Determine voltage probe locations that match BluePyOpt protocols defined with the Neuron simulator using the Arbor graphical user interface (GUI).
72		-Create an arbor.cable_cell and an arbor.single_cell_model or arbor.recipe supporting mechanism catalogues that are consistent with BluePyOpt.
73		-Running a simulation and visualising the results.
74		-=== [[Distributed ring network (MPI)>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_mpi.html||rel=" noopener noreferrer" target="_blank"]] ===
	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.
75	75
76		-//Level: advanced//
77		-
78		-Building a basic MPI aware arbor.context to run a network. This requires that you have built Arbor with MPI support enabled.
79		-Running the simulation and extracting the results.
80		-=== [[Extracellular signals (LFPykit)>>https://docs.arbor-sim.org/en/stable/tutorial/probe_lfpykit.html||rel=" noopener noreferrer" target="_blank"]] ===
81		-
82		-//Level: advanced//
83		-
84		-Recording of transmembrane currents using arbor.cable_probe_total_current_cell
85		-Recording of stimulus currents using arbor.cable_probe_stimulus_current_cell
86		-Using the arbor.place_pwlin API
87		-Map recorded transmembrane currents to extracellular potentials by deriving Arbor specific classes from LFPykit’s lfpykit.LineSourcePotential and lfpykit.CellGeometry
88		-=== [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] ===
89		-
90		-//Level: advanced//
91		-
92		-Building a arbor.context that’ll use a GPU. This requires that you have built Arbor with GPU support enabled.
93		-Build a arbor.domain_decomposition and provide a arbor.partition_hint.
94		-Profile an Arbor simulation using arbor.meter_manager.
95		-=== [[Spike Timing-dependent Plasticity Curve>>https://docs.arbor-sim.org/en/stable/tutorial/calcium_stdp_curve.html||rel=" noopener noreferrer" target="_blank"]] ===
96		-
97		-//Level: advanced//
98		-
99		-=== [[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"]] ===
100		-
101		-//Level: advanced//
102		-
103		-Creating a simulation recipe for two cells.
104		-Placing probes.
105		-Running the simulation and extracting the results.
106		-Adding a gap junction connection.
107		-