Changes for page Arbor

Last modified by abonard on 2025/04/10 15:11

From version 7.1
edited by abonard
on 2025/04/10 15:02
Change comment: There is no comment for this version
To version 11.1
edited by abonard
on 2025/04/10 15:02
Change comment: There is no comment for this version

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34 34  **Level**: advanced(%%) **Type**: user documentation
35 35  
36 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.
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"]] ===
37 37  
39 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
43 +
44 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
48 +
49 +**Level**: advanced(%%) **Type**: user documentation
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"]] ===
53 +
54 +**Level**: advanced(%%) **Type**: user documentation
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 +