
ANATOMICAL CONNECOME MODEL 
Last update: 18/1/2018

This directory contains the MATLAB code implementation of the anatomical model of connectivity in the tadpole spinal cord (this connectome is longer 
than previously published models (see Ferrario et al, 2018). The model uses a developmental approach of axonal growth in a 2D spinal cord envirand a 
numerous amount of experimental data to generate a biologically realisitic map of synaptic connections between neurons in the spinal cord. For 
details about the model formalization and implementation, see Borisyuk et al, PloS One, 2014.

To run one simulation of the anatomical model, run the matlab main_spinal_cord.m file. In this code version, all plotting commands 
are disabled by commenting. This simulation will save the following output files in the "connectome files" directory:

- DendriteGrad1.txt
- inc_connectGrad1.txt
- ALL_synapsesGrad1.txt
- axon_L_ascGrad1.txt
- axon_L_descGrad1.txt
- axon_R_ascGrad1.txt
- axon_R_descGrad1.txt

The description of the data contained in these files as well as manual of how to read them read the file 
"Anatomical Model description.doc" contained in this directory.

To run multiple (parallel) simulations of the anatomical model launch the matlab file run_many_connectomes.m file. 
This file allows to run a user specified number m of anatomical connectomes. For each iteration i=1,...,m the code
runs the anatomical model code via the main_spinal_cord_sub.m subroutine. The code of this subroutine is the same 
as the one contained in the main_spinal_cord.m file, except for the specifications of the returning output files. 
Output of these each main_spinal_cord_sub.m iteration i=1,...,m are:

- DendriteGradi.txt
- inc_connectGradi.txt

These two files are saved in the directory "connectome files", and they are identical to the homonym files 
returned by the main_spinal_cord.m file described above. 






