Now, onto the important part,
OS: Ubuntu 13.10 64-bit
My input to the terminal: "sean@sean-Inspiron-1545:~/Desktop/Neural Networks/Simbrain_2.01$ java -jar Simbrain.jar"
"Exception in thread "main" java.awt.HeadlessException
Exactly the same output for beta 3.0, or release 2.01.
I have jdk7u51 installed and running fine.
I'm more of a C++ and python person, so I have no idea what this error is trying to tell me. Personally, I already don't like the sound of "HeadlessException", as if normal Exceptions weren't annoying enough.
Unfortunately, what you're coming up against is a machine specific error that I can't replicate on my 64-bit Ubuntu machine, so I'm a bit limited in how I can help. However there are a few things you can check and see if it clears up the problem.
This person had a similar problem, which they solved by installing libxtst6:i386... seeing as how that's a 32-bit library, it looks like they might have also been running a 32 bit JRE on a 64 bit machine. So you could try installing libxtst6:i386 or you could make sure that your java is also 64 bit.
Lastly, based on the first link, you could look into your Xorg server and make sure its not telling Java that its headless for whatever reason. This could be in the settings or Xorg could be improperly installed... I couldn't say for sure.
Double checked my Java version, installed the i386 version of that library, and checked and tried reinstalling Xorg, nothing worked.
I think the universe doesn't want me to learn more about neural nets. I literally tried downloading 4 or 5 programs similar to this one, all available for linux, all in different programming languages, and they all had entirely different fatal issues.
Guess I'll just do what I always do in a situation like this; try mimicking this program in Python. Thanks for trying to help anyway. If anyone else can, that'd be appreciated.