
FUNCTIONAL MODEL OF SWIMMING 

This directory contains the updated NEURON code for simulating the dynamics of the initiation, continuation, termination 
and acceleration of swimming in the Xenopus tadpole in response to head and skin touch. The model uses the anatomical 
connectome or probabilistic connectome to generate synaptic connectivity between the neurons in the spinal cord. 
This is a brief description of the files and directory:

- main.py: this is the main code of the simulation. This file contains several routines that create cells, connections, 
  launching a single or parallel (multiple) swimmig simulations and saving results 
- util.py: utility routines for plotting neuron voltages and spike trains, injecting DC current, destroy cells, computing 
  the swimming period and classification of behaviurs
- param.py: file describing physiological model parameters
- nrnMod: folder containing all nrnhoc instances that need to be compiled (via nrnivmodl Neuron syntax)
- nrnTemplate: folder containing cell type specifications in the file CellTemplateCommon.py. This file uses Neuron python
  uses hoc code to create single compartment cells with specified properties, includes methods for generating connections
  between neurons. 
- mp_util.py: code for launching swimming simulations across multiple cores. 
- figures: folder that contains the output of the simulations in folders that are named after current time. 

To easily check if the simulation is running, launch one swimming simulation until 300ms using the following python commands:

import main 
main.SwimmingSimulation(300,1)

This should have generated a new directory in "figures/" which contains output files of the simulations

Launch parallel number (num_process) of stochastic swimming simulations use the following command lines:

RunManySim(num_process)







