II Installation for single workstation use
A/ Installation
First, you need to install the J2SE that you can obtain on the sun webstite. The applications has been run and tested under the 3rd update of 1.5.0. It is not expected to work with earlier Java versions.
You will also need to install Java3D (See java3D for linux if you use Linux, otherwise Java3D for windows is available on the sun webstite).
You then need to create a folder where the following JAR files ought to be:
- jdom.jar (used by the parser) (JDOM). You can find the version used during the development of this application here.
- NML_PLAY.jar
- Holger_modules.jar (the library containing the modules to be used by the application)
- j3dcore.jar, j3dutils.jar and vecmath.jar (Java3D libraries)
A XML file (BasicModel.xml) should also be located in the same folder. It is the default NeuroML file.
If you need to deal with some very large and complicated networks of neurons, you will probably need a network reshaping tool. Such a tool has been included in Reshaper.jar but requires another JAR file called JARInspector.jar (latest version used for the development of this application there 16/03/04). Basically it allows automate shaping of UML diagrams. If you want to use it, please ensure that it is properly licensed. This file should be located in the same folder as the previous files.
Under MS-Windows, you will also need a freeware called pskill (Copyright ? 2000-2005 Mark Russinovich).
B/ Running an application
All the scripts are supposed to be located in the same folder as the JAR files described above.
Under MS-Windows
You can start the application under MS-Windows XP with the following Script (referred from now as NMLPlay.bat)
"C:\Program Files\Java\jdk1.5.0\bin\java" -classpath NML_PLAY.jar;Holger_modules.jar;jdom.jar;j3dcore.jar;j3dutils.jar;vecmath.jar nmlplay.NMLPlay_2
pause
pskill rmiregistry
pskill java
pskill cmd
Set the path in bold appropriately.
Under Linux
You can start the application under Linux on a remote node with the following script Nmlplay. Don't forget to put the correct right on the script Nmlplay by using chmod.
/home/jgrunche/jre1.5.0_01/bin/java
-classpath /home/jgrunche/NMLPLAY/nml_play.jar:/home/jgrunche/NMLPLAY/Holger_modules.jar:/home/jgrunche/NMLPLAY/jdom.jar:/home/jgrunche/jre1.5.0_01/lib/ext/j3dcore.jar:
/home/jgrunche/jre1.5.0_01/lib/ext/j3dutils.jar:/home/jgrunche/jre1.5.0_01/lib/ext/vecmath.jar
nmlplay.NMLPlay_2
You need to put the right Java path instead of /home/jgrunche/jre1.5.0_01. You need to replace /home/jgrunche/NMLPLAY by the path to the root of the application.