Catacomb

Components And Tools for Accessible COomputer Modeling in (neuro)Biology

Version 1.030 Friday January 19 2001

N.B. This version of Catacomb is now frozen, and may not run under the most recent versions of java (since JDK 1.4). The current Catacomb distribution (version 2) is available at www.compneuro.org or at askja.bu.edu.

Catacomb consists of a set of frameworks for various types of models in neuroscience, user interfaces to facilitate building models within these frameworks, and numerical algorithms to compute their behavior. The available frameworks include reaction kinetics, reaction diffusion systems, kinetic scheme models of ion channels, small neuron models and integrate and fire networks.

download/install You can run Catacomb in a java enabled Web browser, but in order to save your own models you need a local copy and a version of the free java runtime environment for your hardware.

documentation It is worth looking at the first two items on the graphical user interface to see how the sliders and the zooming, panning and scaling operations work. There is also a quick reference card in postscript or pdf format.

models Models built with Catacomb. Most of them relate to the book Computational Neuroscience: Realistic Modeling for Experimentalists; Erik de Schutter.

make your own This should fire up Catacomb in a new window, exactly the same as the standalone version except it cannot read or write files. Select a framework from the objects menu and click on its individual components to build up a model. Alternatively, the example models can be loaded from the models menu.
problems How to contact the authors to ask questions, submit bugs or request new features. There is a summary of known problems, upcoming features and questions other people have asked. Also various alternatives if you don't like the user interface, and other features worth looking at from time to time. The tutorials give step-by-step instructions for some of the components.

For Windows and Mac users:

The graphical interface makes extensive use of all three mouse buttons where available. For button challenged mice the following are equivalent:
button 2 == any button with the SHIFT or ALT key held down
button 3 == any button with the CTRL or META key held down

comments, bugs and suggestions to: cannon@inmed.univ-mrs.fr

download/install	You can run Catacomb in a java enabled Web browser, but in order to save your own models you need a local copy and a version of the free java runtime environment for your hardware.
documentation	It is worth looking at the first two items on the graphical user interface to see how the sliders and the zooming, panning and scaling operations work. There is also a quick reference card in postscript or pdf format.
models	Models built with Catacomb. Most of them relate to the book Computational Neuroscience: Realistic Modeling for Experimentalists; Erik de Schutter.
make your own	This should fire up Catacomb in a new window, exactly the same as the standalone version except it cannot read or write files. Select a framework from the `objects` menu and click on its individual components to build up a model. Alternatively, the example models can be loaded from the `models` menu.
problems	How to contact the authors to ask questions, submit bugs or request new features. There is a summary of known problems, upcoming features and questions other people have asked. Also various alternatives if you don't like the user interface, and other features worth looking at from time to time. The tutorials give step-by-step instructions for some of the components.