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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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  • RSME
  • Model Initialization

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  1. Preliminaries

RSME and Model initialization

PreviousSystems Biology Markup LanguageNextModel specification

Last updated 3 years ago

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RSME

RSME is comprised of few main Python files:

  • Functions.py Comprises the many functions used by RSME for model building and simulation

  • SimParameters.py includes the XML parsing engine (described next, in the "model specification" chapter) and various model-specific functions (e.g., synapse dynamics)

  • Simulation.py The main RSME wrapper

  • Stimuli_visual_pattern.py A library containing a set of visual stimulation (e.g., rings of light, drifting bars)

Importantly:

  • RSME generates results and logs in a dedicated Results folder

  • RSME models are specified in hierarchical XML files (described later)

  • RSME uses HOC morphology files (described later)

  • RSME can use precompiled data to accelerate simulation, given as pickle files (described later)

  • RSME uses a short NEURON script named: fixnseg.hoc, used to correct the segment number within each morphological section. You can download the file at the link below.

Model Initialization

To initialize a model you need to import three libraries: NEURON (described earlier), SimParameters, and Simulation:

from neuron import h
from SimParameters import SimulationParameters
from Simulation import Simulation

Following the description of model specification, we showcase various models and simulations.

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fixnseg.hoc