Download the Xholon Tool
Download the Xholon tool from sourceforge. Both the zip file and the tar.gz file include the Java source code and a jar file, complete with all the sample applications. Once you unzip or untar the downloaded file, you will immediately be able to run the examples. Just follow the instructions in README.txt included within the downloaded file. Starting with version 0.6, you can also separately download all the third-party libraries directly from the sourceforge site.
You will also need to download Java, either the Java Standard Edition SDK or JRE, if you don't already have either of these installed on your computer. Xholon has been tested with version 1.4.2 and version 1.5.0. Xholon will also compile with the Java Micro Edition (MIDP) libraries.
Download Third Party Libraries
Xholon can use a number of third party libraries for charts, graphs, and for several specialized purposes. The core part of Xholon, and most of the examples will work WITHOUT any of these packages. You can download this software from the following locations, OR you can download all the third-party libraries as a single file from the Xholon sourceforge site. In all cases the latest version should work as well as some of the earlier versions. You can install the .jar files anywhere on your system, but make sure you edit the Java CLASSPATH in xhn.bat (Windows) or xhn (Linux) in the Xholon home directory.
- JFreeChart is used for line charts and histograms. Xholon will need access to jfreechart-1.x.x.jar and jcommon-1.x.x.jar (for example: jfreechart-1.0.1.jar and jcommon-1.0.0.jar).
- Java Universal Network/Graph Framework (JUNG) is used for network and tree diagrams. Xholon will need access to jung-1.x.x.jar (for example: jung-1.7.2.jar) which can be downloaded just by itself.
- Cern Colt Scientific Library is used for probablity distributions and by JUNG. Xholon will need access to colt.jar and concurrent.jar.
- Apache Jakarta Commons Collections is used by JUNG. Xholon will need access to commons-collections-3.x.jar (for example: commons-collections-3.1.jar).
- The Systems Biology Markup Language (SBML) library, version 2.3.4, is used to transform SBML models into Xholon format. Xholon will need access to sbmlj.jar, which in turn needs access to various libraries that are included with the SBML download. Note that only the xerxes version has been tested with Xholon.
- ECJ for Xholon, a special version of ECJ , a Java-based Evolutionary Computation Research System, is used for genetic programming within Xholon. Xholon will need access to either ecj15_xholon.jar or ecj16_xholon.jar .
- Browser Launcher 2 is used to launch a web browser from the Xholon GUI, to display information about sample applications.