SSA.m

SSA is a Mathematica package that implements Dan Gillespie's
Stochastic Simulation Algorithm for biochemical simulations.

Reference: Gillespie, J. Phys.Chem 81(25):2340 (1977)

Input format is compatible with xCellerator reaction schema, 
but the package can be used independently of xCellerator.

Only unimolecular and bimolecular mass action reactions
are considered.

Examples

   Download zipped Mathematica Notebook
   View in html

Download

To get the latest version, go to http://sourceforge.net/projects/xlr8r/

The release contains the following files:
	
	ssa.nb - source code, not required to run simulations
	ssa.m - a mathematica package, required
	ssa-example.nb - example notebook

Other files may be included in the version of the file release 
that you download.

Install

1. Open Mathematica

2. Type $UserBaseDirectory and note the name of the folder that is 
   returned. Typiucal values will be 

 	~/Library/Mathematica   on Mac OS
	~/.Mathematica on Unix
	C:\Documents and Settings\username\Application Data\Mathematica on
	  Windows

3. In your OS, locate that folder. Verify that there is already a 
   folder "Applications" within that folder. If not, create the folder. 

   Windows users: the Mathematica folder is usually hidden and you will 
   have to type the full folder name into your file browser.

4. Copy the file ssa.m into the $UserBaseDirectory/Applications folder.

5. Each time you start mathematica, if you want to use ssa, you must 
   enter the line 

	<<ssa.m 

   and press enter (Shift-enter on Windows) before you run anything. If
   everything was installed correctly you should see a message like

     SSA 0.1 (22-March-2006) loaded 23-March-2006 17:44:01.320527 using
     Mathematica 5.2 for Mac OS X (June 20, 2005)

   or something very similar.
   
   ( You will need to repeat this step each time you restart 
   Mathematica, unless you install the package in an AutoLoad 
   directory. See the Mathematica Book for more details. )

6. Experienced Mathematica users can install SSA.m in any folder they 
   choose, you are not required to use the folder specified above. To
   make the files visible to all users you should install them in
   $BaseDirectory, rather than $UserBaseDirectory, for example;
   special privelages may be required to do that, however.