*******************README FOR Control of Neural Synchrony Using Channelrhodopsin-2, article tobe published in JCNS 2010********************* Date 11/30/10 : This directory contains all the source codes and other aasociated file for implementing the code and generating figures reported in the JCNS-2010 article titled: Control of Neural Synchrony Using Channelrhodopsin-2-A Computational Study The two main folders containing all the essential libraried are ./C++HH and ./simul_lrn (Do not change or touch any of the libraries in these folders) The main codes are in directory ./C++HH/Codes/OptoControl/ This folder also includes the folder MatlabFiles containing all the relevant matlab scripts as well as the data that was used to generate the figures There are 3 main C++ files. 1)HHOpto.cc 2)PRC.cc 3)Test_Slow_Syn.cc The corresponding executables are 1) runOpto 2) run_PRC 3) run_slow_compute The Makefiles used to create the above executables (compiled on IMAC running i686-apple-darwin10-gcc-4.2.1) are 1) MakeOpto.f 2) Make_PRC.f 3) Make_Inhib_Slow.f All the functions required in above above C++ codes are in define.h and defineOpto.h file. The key Matlabfiles to generate the figures are 1) PlayTemp.m -Creates the Phaseplots of time evolution of delta_n as function of H for various cases presented in the paper 2) CloseLoopTest.m- Does the nonlinear map calculations for closedloop control The full differential equation for the UCI network in the presence of the closed loop control is implemented in Test_Slow_Syn.cc -Sachin S Talathi Assistant Professor Dept of Pediatrics, Biomedical Engineering and Neuroscience Univ of Florida