Wiki source code of Arbor

Version 2.1 by jessicamitchell on 2023/09/11 11:44
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1 Available tutorials:
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
5 //Level: beginner//
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"]] ===
14
15 //Level: advanced//
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"]] ===
25
26 //Level: advanced//
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"]] ===
33
34 //Level: advanced//
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"]] ===
40
41 //Level: advanced//
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"]] ===
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.
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
56 //Level: advanced//
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"]] ===
65
66 //Level: advanced//
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"]] ===
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.