README

This is the readme for the mcell simulation associated with the paper

Keller D, Babai N, Kochubey O, Han Y, Markram H, Schürmann F,
Schneggenburger R (2015) An Exclusion Zone for Ca2+ Channels around
Docked Vesicles Explains Release Control by Multiple Channels at a CNS
Synapse. PLoS Comput Biol 11:e1004253

The directory is organized into supporting subsolders and main
simulations. The supporting subfolders are:

data_files : data waveforms used for driving reaction rates
molecules : the base molecules used in the simulations  
rates : the rates used by the reactions  
geometry_files : geometry of the system  
mechanisms : reactions that the molecules undergo         
parameters : common parameters used by the simulation  

There are four main simulations in the following directories:

small_AZ_random
small_AZ_exclusion       
small_AZ_exclusion_EGTA 
large_AZ_exclusion

Each of these contains a subfolder with an mcell_top.mdl and
variables.mdl file. The main file is mcell_top.mdl and variables
contains variables particular to that simulation.

To run the simulation, change to the subdirectory/1.0 and execute:

mcell mcell_top.mdl

In general, many seeds must be run due to the stochasticity of the
simulation.

Questions can be addressed to: daniel.keller@epfl.ch