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1		-XWiki.abonard
	1	+XWiki.jessicamitchell

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	1	+Available tutorials:
1	1
	3	+=== [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
2	2
3		-* ((( ==== **[[Beginner >>||anchor = "HBeginner-1"]]** ==== )))
	5	+//Level: beginner//
4	4
5		-* ((( ==== **[[Advanced >>||anchor = "HAdvanced-1"]]** ==== )))
	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"]] ===
6	6
7		-=== **Beginner** ===
	15	+//Level: advanced//
8	8
9		-=== [[Arbor Tutorial Index – from Cells to Networks>>https://docs.arbor-sim.org/en/latest/tutorial/index.html||rel=" noopener noreferrer" target="_blank"]] ===
	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"]] ===
10	10
11		-**Level**: beginner(%%) **Type**: interactive tutorial
	26	+//Level: advanced//
12	12
13		-=== [[A simple single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_model.html||rel=" noopener noreferrer" target="_blank"]] ===
	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"]] ===
14	14
15		-**Level**: beginner(%%) **Type**: user documentation
	34	+//Level: advanced//
16	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** ===
	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"]] ===
20	20
21		-=== [[GPU and profiling>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring_gpu.html||rel=" noopener noreferrer" target="_blank"]] ===
	41	+//Level: advanced//
22	22
23		-**Level**: advanced(%%) **Type**: user documentation
	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"]] ===
24	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.
	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.
26	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	27
28		-**Level**: advanced(%%) **Type**: user documentation
	56	+//Level: advanced//
29	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.
	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.
37	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"]] ===
38	38
39		-**Level**: advanced(%%) **Type**: user documentation
	66	+//Level: advanced//
40	40
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"]] ===
	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"]] ===
43	43
44		-**Level**: advanced(%%) **Type**: user documentation
	76	+//Level: advanced//
45	45
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.
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"]] ===
	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"]] ===
48	48
49		-**Level**: advanced(%%) **Type**: user documentation
	82	+//Level: advanced//
50	50
51		-This tutorial will guide you through to create an ion channel with NMODL from scratch through a classic Hodgkin-Huxley ion channel model.
52		-=== [[A detailed single cell model>>https://docs.arbor-sim.org/en/stable/tutorial/single_cell_detailed.html||rel=" noopener noreferrer" target="_blank"]] ===
	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"]] ===
53	53
54		-**Level**: advanced(%%) **Type**: user documentation
	90	+//Level: advanced//
55	55
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.
57		-=== [[Synapses in NMODL>>https://docs.arbor-sim.org/en/latest/tutorial/nmodl.html#synapses-in-nmodl||rel=" noopener noreferrer" target="_blank"]] ===
	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"]] ===
58	58
59		-**Level**: advanced(%%) **Type**: user documentation
	97	+//Level: advanced//
60	60
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.
62		-=== [[A ring network>>https://docs.arbor-sim.org/en/stable/tutorial/network_ring.html||rel=" noopener noreferrer" target="_blank"]] ===
	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"]] ===
63	63
64		-**Level**: advanced(%%) **Type**: user documentation
	101	+//Level: advanced//
65	65
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.
	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.
67	67