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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"]] ===
	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"]] ===
33	33
34		-**Level**: advanced(%%) **Type**: user documentation
	66	+//Level: advanced//
35	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.
	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"]] ===
37	37
	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	+