Catacomb 2 Examples

These help pages are best viewed from within Catacomb 2, in order for the files to be loaded automatically and the commands to take effect when you click the corresponding links. To do this, start Catacomb and select open web page from the file menu. Accept the default address if you have a web connection. Otherwise you must be reading them locally, in which case, copy the current URL (it should begin "file:/") into the address to be opened.

The examples are in roughly increasing order of complexity. The first two sections on the workbench and lab equipment are necessary to understand the rest but after that the order is less important.

• Workbench Basics. How to build models with the workbench - different operating models, component sets, setting parameters and displaying results.
• Lab Equipment. Generating and recording continuous signals and spikes.
• Data flow and Logic Functions. Splitting and reconnecting vectors; redistributing spikes; programming spike sequences.
• Integrate and Fire Cell Models. Adding properties to a simple integrator to make progressively more subtle cell models.
• Grouping and Reusing Components. Perhaps the most important feature if Catacomb 2 is its ability to group components and connections into new types of processing unit. These can then be used exactly like the elementary components. This way you can build structured hierarchical models without any duplication of effort.
• Populations of Cells. A cell population is the basic construct for most network models. There are special components for defining projections between populations without putting in the separate connections one by one.
• Virtual Environments. Walls, sound sources, food dispensers et al. for setting up a behavioral experiment; Sensors and effectors for building a "robot" to experiment on.
• Animats. More circuitry for interfacing animats to the virtual environments.
• Synapses. Spikes arriving at a synapse trigger processes leading to conductance changes in the post-synaptic cell. These can be modeled at a variety of levels in Catacomb, including timing dependent plasticity functions and transmission modulation by external agents.
• Membrane Channels. In Catacomb2 integrate-and-fire models merge smoothly into channel-based models. You can mix and match components according to the behavior you want to study.
• Accessing the CoCoMac database. Catacomb2 includes an experimental interface to the CoCoMac database of connectivity in the macaque.
• Jython Scripts. As a last resort, where you can't get the functionality you want from the existing components, there is a "black box" for holding code written in Jython.
• Hierarchical Groups. The grouping system works on compound objects as well as sinmple components, so you can make hierarchically structured models. The main new concept here is how you connect external components to different parts of the hierarchy.