Files to reproduce figures from a previous version of:

"Soudry D and Meir R (2014) The neuronal response at extended timescales: 
a linearized spiking input–output relation.
Front. Comput. Neurosci. 8:29. doi: 10.3389/fncom.2014.00029"

Note that during the review process some modifications were made to code and figures. 
I have not yet uploaded this changes.

Simulation Folder:
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* Simulation of Full stochastic Conductance based models described in article:

Simulation_HHMS
Simulation_HHMS_Poisson
Simulation_HHMSIP
Simulation_HHS
Simulation_HHS_Poisson
Simulation_HHSIP
Simulation_HHSTM
Simulation_MHHMS

* Simulation of the excitability map for HHS model:

Simulation_Excitability_Map

Plot_Figures Folder:
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This files in this folder handle the process of generating of the figures in paper
from the data generated by the simulations.
Note that in order to do this, the relevant simulations are needed to be run 
first and generate the data files (which are quite large, since the simulations 
are quite long - usually about 55hrs). Then, the location and name of these data 
files are needed to be updated the "update_arrays" and "GetLocation" functions 
in the "Data_array" class, located in the "Class_files" subfolder.

* Main folder files handle the generation of the final figures in paper:

Math_Fig_HHS
Math_Fig_Limits
Math_Fig_p_s
Math_Fig_SY
Math_Fig_SYT_full

* Plot_Figures\Predictor_Performances sub-folder:

Predictor_Performances.m - generates performance tables for AP predictors
Other (data) files - various performance tables previously generated


* Plot_Figures\p_star sub-folder:

Get_p_star.m - generates p_star tables for different models
Other (data) files - various p_star tables previously generated

* Plot_Figures\Class_files sub-folder (used to generate figures):

Data_array  - update here location and names of data files in "update_arrays" and "GetLocation" functions
Data_source
Get_Plot
Graphic_Specs
Model
Parameters
Predictor
Predictor_Performances
Rates

* Plot_Figures\Class_files\p_s_functions sub-sub-folder:

- These files estimate empiric p_{AP}(s) for all used models
  (HHMS and MHHMS use HHS's, and HHMSIP use HHSIP's):

Get_Prob_coupled_HHS
Get_Prob_HHS
Get_Prob_HHSIP
Get_Prob_HHSTM

- These files average out several repetitions of previous files
  and generate and analytic p_{AP}(s) (which is used by the model class)

Combine_Reps_coupled_HHS
Combine_Reps_HHS
Combine_Reps_HHSIP
Combine_Reps_HHSTM

Other (data) - previously generated p_{AP}(s) functions

* Plot_Figures\Class_files\Averaged_Rates sub-sub-folder:

These files estimate the relevant averaged rates for the "excitibility map" for all models used

Get_Average_rates_HHS.m
 - auxilary functions: hhx.m, beta.m, alpha.m
Get_Average_rates_HHSIP.m
 - auxilary function: get_params.m
Other (data) files - various averaged rates previously generated