Interface to the NewTMaze model in Catacomb2

The original model was developed in Catacomb 2.034, and can still be run through that version of Catacomb 2, though not with later versions because of non-compatible changes in file formats and component specifications.

The present version (see the home page for the latest jar file) consists if a Catacomb 3 framework that lets you specify a few of the key parameters. It runs the model with the original values replaced by the new ones, and extracts selected results to display. You can also access the original (Catacomb2) interface any time to access more of the model.

Getting started

You run the jar file by typing java -jar catacomb3alpha1.jar under linux, or by double clicking under windows. If nothing happens check that you have got the latest version of Java from java.com. You need version 5.0 - at present (January 2006) it is called "Java Runtime Environment Version 5.0, update 6".

It will asks for a folder where the models and frameworks can be stored. The file chooser lets you make a new folder, or you can just accept its suggestion.

The main window has a tree on the left showing the contents of the models folder. Initially it shows just the one model that is included with the distribution.

To open a particular model, just click on it in the tree on the left. The NewTMaze model is rather unusual because when you open it, it starts Catacomb2 and loads the original model. This takes several seconds, so it is normal for the display to freeze there for a while.

Once the model is loaded, it appears in the middle panel in view mode where you can see a description of the model and, at the bottom, a summary of the parameters in the model. Again, this is a little unusual, because the only parameters here are the four delays. Everything else is in the original model.

The edit button at the top switches into editing mode where you can modify parameter values. By clicking on the labels, you can read more about a parameter (bottom right of the main window). The edit button next to the ccmb2Wrapper field starts the original Catacomb 2 interface.

The main panel to the right is for running a model. It shows that there is one calculation defined for the model. The calculation can be started with the run button at the right. As it proceeds, you should see results popping up in the list below. This calculation extracts a few key quantities from the Catacomb2 session - the rest can be accessed through the original interface.

Three of the result sets are spike rasters from the main populations in the model. The other shows a movie of the progress of the rat. To view the movie comfortably you may need the F (for frame) button at the top right to get it all in the picture, and the little f button at the lower left to make it faster. Alternatively, pulling the slider lets you jump to particular frames.

Advanced

You can access the framework that defines this model by switching to the components view. There are only two components included with this version: the framework specification itself, and a specification of how the model is run (what java class file to use etc).

The framework is fully editable. Changes to the textual information (such as the descriptions of parameters) can be made freely and will show up in the help text of the model editor. You can also add new parameters or structures to the framework. These will appear in the model but will require some corresponding changes in the source code (the class mentioned in the implementation specification) before they have an effect on the way the model is run.