******************************************************************************
 
                             CalC version 6.0.5 
               Calcium diffusion, buffering and binding solver
                   Developed at MRB/NIDDK/NIH and at NJIT
 
                               Victor Matveev
                         Dept of Math Sciences, NJIT
                               matveev@njit.edu
                       http://web.njit.edu/~matveev

                             September 24, 2008

******************************************************************************
==============================================================================
                             1.  COMPILATION
==============================================================================

1) Windows: 

   If the stand-alone executables "calc_win32.exe" and "calc_cygwin.exe" are not 
   working, download and unzip the file "calc_win32_6.0.5.zip". It contains the source
   code (subdirectory "source"), the example script files (subdirectory "examples"),
   and a distribution of the "gnuplot" package for plotting the results. You have
   to use MS Visual Studio to compile the code. Alternatively, you can install 
   "cygwin" (http://www.cygwin.com") on your Windows machine, which is a Linux 
   emulator for Windows. This would enable you to install the unix version of 
   the program, and use its xmgrace graphics capabilities (provided you install the
   xmgrace, make, g++ and X11 windows packages supplied by cygwin sites).

2) UNIX platforms (including cygwin and OS X)

  Place the downloaded archive into a new separate directory,
  then unpack and compile it using:

    gunzip calc_unix_6.0.5.tgz
    tar xf calc_unix_6.0.5.tar
    gmake 

  If "gmake" does not do anything, try "make".

3) Mac OS X users: you will need to install g++ and the gnu make utility in order
   to be able to compile the Unix version of the code. The gnu make utility is
   available at http://web.njit.edu/~matveev/calc/gmake-3_79_1-Mac_OS_X.tar.gz


==============================================================================
                             2.  EXECUTION:
==============================================================================

1) Windows: 

Open a DOS window (Start Menu -> Run -> "cmd"), go to the directory where
the executable "calc_win32.exe" is residing, and type "calc_win32.exe filename", 
where "fileName" is the name of the script file describing the simulation. Note 
that a simulation script may require command-line parameters (see
http://web.njit.edu/~matveev/calc/manual.html#pars ). Alternatively, you can
simply click on the "calc_win32.exe" file. 

2) Unix platforms:

Execute "calc fileName", where "fileName" is the name of the script file 
describing the simulation. Command-line parameters may be required by the
simulation script (see http://web.njit.edu/~matveev/calc/manual.html#pars ).

==============================================================================
                             3.  DATA OUTPUT:
==============================================================================

o All platforms: 

Simulation results can be saved to a file in real time using "mute" plot 
statements, ASCII files are produced that are readable by both gnuplot or 
MATLAB. Refer to http://web.njit.edu/~matveev/calc/manual.html#mute for details.

  Gnuplot can be downloaded from
  http://www.duke.edu/~hpgavin/gnuplot.html

o UNIX platforms: 

It is recommended that you use the "xmgr" or "xmgrace" graphics applications,
which allow viewing the simulation results in real time. This involves piping
the program output into xmgr or xmgrace, by executing
"calc scriptFileName | xmgr -pipe" (or "calc scriptFileName | xmgrace -pipe"),
where "scriptfileName" is the name of the simulation script. In this case the 
script file should contain an instruction "plot.method xmgr". To do the piping 
automatically, you can use the supplied scripts "calcgr" and "calcgrace" 
(i.e., execute "calcgr scriptFileName" or "calcgrace scriptFileName").

  Xmgrace can be downloaded from
  ftp://plasma-gate.weizmann.ac.il/pub/grace/

  Xmgr can be downloaded from 
  ftp://plasma-gate.weizmann.ac.il/pub/xmgr4/

o Windows platforms: 

Use "mute" plots to produce data files, which can then be plotted using MATLAB
or gnuplot. Alternatively, install "cygwin" (http://www.cygwin.com"), a Linux
emulator for Windows, which would enable you to install the unix version of
CalC, and use its xmgrace graphics capabilities.

==============================================================================
                             3. DOCUMENTATION:
==============================================================================

o  A hyper-text CalC script syntax manual can be found at URL
   http://www.calciumcalculator.org

o  Also, included are commented example script files (file extension 
   ".par"): they reside in the "examples" directory.

******************************************************************************
==============================================================================