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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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Model specification

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Last updated 3 years ago

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RSME comprises a NeuroML- inspired XML-based specification interface and a dedicated parsing engine, which supports detailed biophysical, morphological, network architecture, and stimulation parameters. It features a set of mechanisms for retinal circuitry-related specifications.

Learn about NeuroML in:

Model specification is mostly based on several XML files, as it is detailed below. Note that some model parameters are specified in the code, and not in the XML. Those parameters are used to optimize the model using a genetic algorithm as will be discussed later.

Learn more about XML files and their Python-based processing in:

When the RSME model is initialized, the path for the XML files should be provided. We recommend creating a "simulation_parameters" folder inside the project directory. Inside this folder, create five XML files

NeuroML - A Model Description Language for Computational Neuroscience
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xml.etree.ElementTree — The ElementTree XML API — Python 3.8.12 documentation
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