Model specification

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:

NeuroML - A Model Description Language for Computational Neuroscience

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:

xml.etree.ElementTree — The ElementTree XML API — Python 3.8.12 documentation

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