This page will look better in a graphical browser that supports web standards, but is accessible to any browser or internet device.

Served by Gloin.

Installing JSim under Microsoft Windows

JSim's Windows distribution runs on Windows 10, Windows 7, and Windows XP. JSim is not tested on Windows Vista but has run successfully on it in the past.

  1. Download the appropriate JSim zip archive. Providing the following information will help us demonstrate JSim's continued utility to the funding agencies upon which we rely. Filling out this form will not result in your addition to any mailing lists other than a JSim usage survey that is sent once a year. Your response to that survey will help us to retain our funding. If you wish to receive news about JSim on a more frequent basis, please contact us.


    JSim is free for non-commercial use. View complete license terms

    • Note: Internet Explorer(IE) users have sometimes noted that JSim download hang for several minutes at 99% complete. This appears to be a bug in IE. Our experience is that, if the user is patient, the download completes successfully after about five minutes.
  2. 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'
  3. Inside your installation folder, you will find a sub-folder win32\bin containing the following executable files:
    • jsim.bat : the JSim GUI application (First-time users use this one).
    • 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.

  4. 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.
  5. 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.
  6. 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.
  7. Windows 10 and high resolution screens : If your computer is running MS Windows 10 and has a screen resolution greater than 1080p (1920x1080) JSim may look really tiny and unreadable. This scaling issue can often be fixed by passing a Java flag turning off scaling when starting JSim. The Java 1.6 flag to use is "-Dsun.java2d.dpiaware=false". Insert it into the following line of jsim.bat file:

    %JAVA% "-Dsun.java2d.dpiaware=false" "-Djsim.home=%JSIMHOME%" -Xmx%JSIMMEM%m "-Djava.library.path=%JSIMNATIVE%" -Djsim.userdir=HOME JSim.gui.GLaunch %*

  8. 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

  9. Optional advanced administration:

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.

This regrettable situation is unavoidable given the design of Windows, and is made worse by Microsoft refusing to give information to developers (outside of Redmond) as to how exactly the registry works. Therefore, you may need to muck with your registry a bit manually to get things just right. jsreg.bat is written so you can examine what is being done, and modify it if you are so inclined. If you relocate JSim on your system, rerunning jsreg.bat will repoint the registry appropriately.

Comments or Questions?

[This page was last modified 30Dec16, 11:48 am.]

Model development and archiving support at provided by the following grants: NIH/NIBIB BE08407 Software Integration, JSim and SBW 6/1/09-5/31/13; NIH/NHLBI T15 HL88516-01 Modeling for Heart, Lung and Blood: From Cell to Organ, 4/1/07-3/31/11; NSF BES-0506477 Adaptive Multi-Scale Model Simulation, 8/15/05-7/31/08; NIH/NHLBI R01 HL073598 Core 3: 3D Imaging and Computer Modeling of the Respiratory Tract, 9/1/04-8/31/09; as well as prior support from NIH/NCRR P41 RR01243 Simulation Resource in Circulatory Mass Transport and Exchange, 12/1/1980-11/30/01 and NIH/NIBIB R01 EB001973 JSim: A Simulation Analysis Platform, 3/1/02-2/28/07.