web browswer. There is also a pure java version available that
supports most though not all features of <tt>iBioSim</tt>. This is a good option when having trouble with the other installations, since it is machine independent.
To install the pure Java version, you need to download <tt>iBioSim-2.8-Java.zip</tt> and unzip it in the directory you wish to install. The <tt>iBioSim.jar</tt> file should be executable, but may require being invoked using the explicit command: <tt>java -jar iBioSim.jar</tt>.
The <tt>iBioSim.mac64</tt> script makes it look better on Mac environment.
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<h2><aname="tth_sEc3">
3</a> MacOS Installation</h2>
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To install on MacOS, you need to download <tt>
iBioSim-〈version〉-MacOS.dmg</tt> file. You should then
open this file with <tt>DiskImageMounter.app</tt>. This should open up
this disk image in <tt>finder</tt>. You should then copy the contents of
this disk image to your Applications folder. You should then be able
to start <tt>iBioSim</tt> by double-clicking on this application.
In your start menu, there should be an option to uninstall. If you
select this, it will ask if you are sure then proceed to completely
remove <tt>iBioSim</tt> from your system. It is highly recommended that
you remove <tt>iBioSim</tt> using this uninstall procedure before
installing a new version.
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Note that since there are a large number of different linux installations, there can be problems especially with older installations. If you are having problems though, first log out and back in. There are some environment variables that need to be set. If you are still having problems, then read on.
Our linux installations are currently built for 32-bit and 64-bit versions of Fedora 15. While the Java parts of our program port smoothly, there are often issues with the dynamic libraries and the C/C++ programs <tt>reb2sac</tt> and <tt>GeneNet</tt>. If you are having a problem, the first step is to download and build libsbml Version 5.0. You will need to replace the libsbml.so* and libsbmlj.so files with your build of libsbml in either lib or lib64 depending on whether you are using a 32-bit or 64-bit machine. At this point, you should be able to start <tt>iBioSim</tt>. However, if you are still having problems, send an email to <tt>myers@ece.utah.edu</tt> including information about your OS and any error messages when you try to execute <tt>iBioSim</tt> from the command line.
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You should also now test <tt>reb2sac</tt> and <tt>GeneNet</tt>. In your install directory, try the following:
