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Retinal Stimulation Modeling Environment
  • Retinal Stimulation Modeling Environment (RSME)
  • Preliminaries
    • Python
    • NEURON
    • Systems Biology Markup Language
    • RSME and Model initialization
  • Model specification
    • Meta-parameters
    • Morphology Description
    • Network Description
    • Visual Stimulation
    • Biophysical Description
  • Visual Stimulation
  • Single SAC model
    • Model Initialization
    • Model Visualization
    • Model Simulation
  • SAC plexus model
    • Before we begin
    • Model Initialization and Visualization
    • Model Simulation
  • SAC-DSGC network
    • Model initialization and visualization
    • Model Simulation
  • Logger
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  1. Single SAC model

Model Initialization

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Last updated 3 years ago

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You can download the XML specifications for this model here:

Following library imports as was described earlier in the preliminaries, a model is initiated using:

simulation_parameters = SimulationParameters(
    "simulation_parameters/single_SAC_meta.xml",
    note = 'single_SAC')

RSME is therefore initialized with a path to the meta-parameters XML file and a note. The note is used to identify the model and generate a log with an identifiable name. For example, when executed, RSME will create a new subfolder (withing Results) named: "RSME_19_15_05-07_10_2021_single_SAC_9031769193263726". The name includes the date, time, note, and a unique identifier (randomly generated) for your simulation results.

Use the model specification to initiate a new simulation:

simulation = Simulation(simulation_parameters)

When a specific configuration runs for the first time, RSME will create a new pickle file, containing illumination events for the specified model and visual stimulus. It might take it a while to create this file (depending on the model's morphological complexity), however, next time you run it, RSME will load the stimulation data from this final, dramatically improving runtime.

In this case the generated file is: possible_stimulation_trains_single_SAC_meta.xml_lightdt0.2.p

5KB
single_SAC.zip
archive