A Quick Tour of Catacomb2

Using the Workbench

The figure shows the workbench in action with a simple cell model.

On the left are parameters of the workbench itself. On the right are the parameters of the active component. In the middle is the model.

The buttons at the very top, show what sets of components are currently available. Click a button for the corresponding components to be presented at the top of the window. Click it again to hide the set. When a component is visible you can use it simply by dragging it off the row with the mouse.

Editing Modes

There are five small graphics at the bottom right of the work area showing the possible operating modes. The active mode is shown with a whit background. Click on a different one to change the mode. They work as follows:

• Build mode - used for constructing models. You can attach connectors and resize components by dragging the bottom left or top right corners. You can also move components by clicking on a point where the whole component is highlighted.
• Move mode - just for moving components around. The other control points have been inactivated so it is easier to move things around without changing their size or disconnecting cables.
• Run mode - a different set of points are active in run mode, corresponding to the knobs and switches on the components. (***Dec 2001 - there are very few of these so far***)
• Help mode - click on any component to show its on-line help.
• Delete mode - for removing (permanently) components of the model.

Model components

The basic set of components (as if December 01) is shown below. At any time you can save a section of the current network as a new component. It will then appear in the menus as a new type of unit.

The first button, "link" contains a set of essential components for any model - the different types of connections that can be made between the components. Once you drag a component onto the workbench, a number of small dots appear on it showing the ports where connections can be made. Click on an object with the right mouse button to show the names of the ports. The colors also indicate what connections are meaningful, and correspond to the colors of the different types of link.

• Vector Cables propagate a set of values from one port to another. It is up to the receiving component to do what it wants, when it wants, with the data.
• Spike Cables propagate spikes (events occurring at a particular time) between components. Because the time of occurrence is important, the receiving component typically acts immediately when a spike arrives.
• Tubes are for liquids: whatever is present at one end gets taken to the other.
• Cords are for tying things together where, in reality you might use string, scotch tape or the like. For example, in designing a robot, the various sensors and effectors are connected together with cords.
• Insertion Arrows show where something is inserted in something else. They are used, for example, in inserting membrane channels in the membrane of a cell, or for showing where in an environment a food dispenser should be placed.

The next set of components are standard lab equipment - signal generators, spike generators, switches, buttons bottles and recording devices. The "logic" shelf contains things which may be useful for controlling data flow around the workbench. It also has components to perform certain tasks, like feature discretization, which in a real animal would be done by a neural system. This is a standard feature of the modeling approach: to use software modules to perform certain tasks in the model so attention can be focused on making biologically relevant models of the parts of the system under study.

Mouse Scaling

Like most of the windows in Catacomb2, the whole workspace can be panned and zoomed with the mouse. There is also a little menu at the top right with a number of handy functions in it. The capital letters indicate keyboard shortcuts. Finally, the "Helper" option under that menu gives access to a few more properties of the window. In particular, you can switch off the mouse scaling until you have got the hang of it.