Phase Response Curve Modeling Package
Version 2.7 by Dmitri Pervouchine
Date: Dec 20, 2008
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1. INSTALLATION
   To install, first unzip the package by typing the following two lines into the command line:

	gunzip strcpackage.tar.gz
  	tar - xf strcpackage.tar

   Next, enter the target directory and type:

   make all

   As a result of this action, you will get a set of executable binary files.

   Note: depending on your system configuration, you might get error messages during compilation. If so, 
        please consult your local LINUX guru about the usage of C++ compilers on your machine.  This software 
	is provided "as is" and DOES NOT ASSUME ANY KIND OF WARRANTY 

2. PACKAGE ARCHITECTURE 
   
   The package consists of the following files:
   
   neuron.c, neuron.h - the neuron library package
   models.c, models.h - package extension including models of interneurons, pyramidal, and O-LM cells
   tables.c, tables.h - auxiliary functions for tabulation of EXP function (this speeds up computations significantly)
   function.c, function.h - auxiliary package for superposition of real functions

   i_init_cond, i_init_cond0, i_init_cond1, i_init_cond2 - initial conditions for the I-cell
   o_init_cond, o_init_cond0, o_init_cond1, o_init_cond2 - initial conditions for the O-cell
   e_init_cond0, e_init_cond1 - initial conditions for the E-cell

   strc_I2O.c, strc_O2I.c, strc_O2O.c, strc_O2E.c, strc_PING2O.c - scripts for PRC generation
   analyze.c - script for generation of STDMs

   figs.m - MATLAB file to generate figures as they appear in the text

   manual.pdf - additional information on package architecture

   output - directory with sample PRC output files generated by the package

3. USING THE PACKAGE

   The scripts strc_I2O, strc_O2I, strc_O2O, strc_O2E, and strc_PING2O are simple examples of how
   the neuron library package can be used to generate STRCs (follow line-by-line comments in strc_I2O.c; the
   other scripts don't have line-by-line comments). Each script generates a family of STRCs with different 
   values of the synaptic conductance. The result is saved in a tab-delimited .out file (see output/). These
   text files are then read by the "analyze" script to generate STDMs (analyze.c contains line comments).

   To generate STRCs and STDMs, type in the LINUX command line:

   make results

   This will run simulations encoded in strc_I2O, strc_O2I, strc_O2O, strc_O2E, strc_PING2O, and analyze scripts.

   Note: the output written to stderr is to indicate the progress since the entire set of simulations may 
   take a long time.

   As a result, you will get a collection of tab-delimited .out files.

   To visualize STRCs and STDMs as they appear on the page, run the figs.m MATLAB script. 

4. Question, comments, or suggestions can be mailed to dp@bu.edu
