chaptersoftware

contents software data java models

Copies of public domain packages for local installation

Neuron Neuron is a powerful and flexible environment for modeling neurons and networks. It runs under MacOS, Windows and UNIX. Neuron's Web site is http://www.neuron.yale.edu/

Genesis Genesis is also a powerful and flexible environment for modeling neurons and networks. It runs under UNIX. The home site is http://www.bbb.caltech.edu/GENESIS

Catacomb Catacomb (Components And Tools for Accessible COmputer Modeling in Biology) is not a powerful and flexible environment, but a set of components for modeling biological systems and graphical interfaces to interact with them. This version is aimed at small relatively simple models. It includes example models for several chapters of the CD-ROM. These can be run via a web browser but they run best if you install the Java Runtime Environment. It is under active development and you can get the latest version from compneuro.org.

XPP GUI based package for studying dynamical systems.
From the XPP tutorial:

Dynamical systems theory provides the language and the machinery for the analysis and understanding of the behavior of physical systems that change over time. There are many ways in which such systems can change and many types of equations that arise. These include discrete and continuous dynamical systems.

XPP can handle

Differential equations
Delay equations
Volterra integral equations
Discrete dynamical systems
Markov processes
Bifurcation

Cvapp Cvapp was originally written to clean up and standardize neuronal morphology data. Since then it has been extended to perform a variety of other functions, including converting from the format used by the neuron tracing program Neurolucida to those used by Neuron and Genesis. The original version is included here as part of the morphology archive but this is a new improved version by Steve Van Hooser which includes several features specifically for modeling with Genesis, particularly the ability to rediscretize the structure. Dieter Jaeger has written _LINKS(cvapp/dieter.html) detailed instructions on how to use this version.

Java The Java Runtime Environment (JRE) lets you run java programs. It is freely redistributable, unlike the Java Development Kit which also lets you compile your own programs. Versions of the latter are also freely available, but under different conditions. Here you will find the JRE for Windows and Linux. Javasoft have links to development kits for many platforms.

Yorick Yorick is a high-level interpreted language for array based numerical computing, data analysis and visualization with c-like syntax. It is a little like IDL and matlab but is freely redistributable.
The Yorick manual provides an introduction to using yorick.
For UNIX platforms, the standard distribution needs patching with the latest updates. This has already been done on the file yorick-1.4.tgz. To install it the instructions below should be sufficient. There is also a program rlterm distributed with Yorick which is well worth installing - see instructions in the Yorick directory.

gzip -d yorick-1.4.tgz
tar xvf yorick-1.4.tar
cd yorick-1.4
./configure --prefix=here
make
make check
make install


Neuron	Neuron is a powerful and flexible environment for modeling neurons and networks. It runs under MacOS, Windows and UNIX. Neuron's Web site is http://www.neuron.yale.edu/

Genesis	Genesis is also a powerful and flexible environment for modeling neurons and networks. It runs under UNIX. The home site is http://www.bbb.caltech.edu/GENESIS

Catacomb	Catacomb (Components And Tools for Accessible COmputer Modeling in Biology) is not a powerful and flexible environment, but a set of components for modeling biological systems and graphical interfaces to interact with them. This version is aimed at small relatively simple models. It includes example models for several chapters of the CD-ROM. These can be run via a web browser but they run best if you install the Java Runtime Environment. It is under active development and you can get the latest version from compneuro.org.

XPP	GUI based package for studying dynamical systems. From the XPP tutorial: Dynamical systems theory provides the language and the machinery for the analysis and understanding of the behavior of physical systems that change over time. There are many ways in which such systems can change and many types of equations that arise. These include discrete and continuous dynamical systems. XPP can handle Differential equations Delay equations Volterra integral equations Discrete dynamical systems Markov processes Bifurcation

Cvapp	Cvapp was originally written to clean up and standardize neuronal morphology data. Since then it has been extended to perform a variety of other functions, including converting from the format used by the neuron tracing program Neurolucida to those used by Neuron and Genesis. The original version is included here as part of the morphology archive but this is a new improved version by Steve Van Hooser which includes several features specifically for modeling with Genesis, particularly the ability to rediscretize the structure. Dieter Jaeger has written _LINKS(cvapp/dieter.html) detailed instructions on how to use this version.

Java	The Java Runtime Environment (JRE) lets you run java programs. It is freely redistributable, unlike the Java Development Kit which also lets you compile your own programs. Versions of the latter are also freely available, but under different conditions. Here you will find the JRE for Windows and Linux. Javasoft have links to development kits for many platforms.

Yorick	Yorick is a high-level interpreted language for array based numerical computing, data analysis and visualization with c-like syntax. It is a little like IDL and matlab but is freely redistributable. The Yorick manual provides an introduction to using yorick. For UNIX platforms, the standard distribution needs patching with the latest updates. This has already been done on the file yorick-1.4.tgz. To install it the instructions below should be sufficient. There is also a program `rlterm` distributed with Yorick which is well worth installing - see instructions in the Yorick directory.