Installing JSim under Microsoft Windows

JSim's Windows distribution runs on Windows XP and Windows 7. JSim is not tested on Windows Vista but has run successfully on it in the past.

1. Unpack the .zip file using your system's ZIP utility in a folder of your choice.
   • Note: You may need administrator privileges to install JSim into certain system directories such as 'Program Files'
2. Inside your installation folder, you will find a sub-folder win32\bin containing the following executable files:
   • jsim.bat : the JSim GUI application;
   • jsbatch.bat : the JSim text-based batch application.
   • jsfim.bat : the JSim functional imaging application.
   • jsserver.bat : the JSim remote server application.
   • jsreg.bat : adds JSim settings to the Windows registry
   • reg.exe : general purpose Windows registry tool used by jsreg.bat

   You may wish to make a short-cut to jsim.bat on your Desktop, or other convenient location. Other executables are useful only from the Windows command prompt.

3. JSim 2.07 and above requests 1500MB of heap memory by default. If your system has less than 2GB of memory, you will probably need to reconfigure JSim to use less memory before JSim can launch properly.
4. The optional jsreg utility sets your Windows registry so that certain JSim files (e.g. .proj) are loaded into JSim when double-clicked. See here for more information.
5. Most users do not require the command-line utilities jsbatch.bat and jsfim.bat, which require some additional setup. If you do, do as follows (familiarity with .bat files and the DOS command line is assumed): In a text editor, modiry the PATH environment variable to include the directory containing jsim.bat and jsbatch.bat. Also, modify the JSIMHOME definition in jsbatch.bat or jsfim.bat to the the device:directory you have chosen for your JSim installation.
6. SBML, Antimony, and Matlab users: JSim dynamically links to its own version of libsbml.dll. If you have a previously installed version of libsbml.dll in the Windows system dir (ie c:\windows\System32\) then JSim will not be able to load the correct dll and you will get an error when using JSim to translate models to/from SBML, to/from Antimony, and generating Matlab code. The current work-around is to install your previous version of libSBML into another directory and remove/rename libsbml.dll from the Windows system directory. Evidence of this issue is a 'libSBML native library not found' message displayed from within the JSim application or a more detailed message at the console like this:

   java.lang.UnsatisfiedLinkError: C:\..\sbmlj.dll: The specified procedure could not be found

Using jsreg.bat

jsreg.bat adds settings to the Windows Registry that allows you to open .proj, .tac and .jsml files within JSim by double-clicking on their icons in Windows Explorer. These settings can cause problems for other programs in your system if they expect to open files with those same extensions. Conversely, the opening of files with those extensions within JSim can be impaired by other programs.

• Windows 7 - jsreg.bat must be run with administrator privledges. To do this either right mouse-click jsreg.bat and pick 'Run as adminstrator' or run cmd.exe as administrator and execute jsreg.bat at the command line.
• After running jsreg.bat you must reboot your computer to refresh the icon file associations.
• JSim .mod (models) extension conflicts with MS Windows use of .mod for media files. Double-clicking a JSim .mod file will not open up JSim by default. You must chose it explicitly.