RSME and Model initialization

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.

1KB

fixnseg.hoc

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.