Here are some software packages I have developed during my work, some on my own, other in collaborations. All software is available under open source licenses. I would like to hear from you if any of my work was useful to you!

NEST: Neural Simulation Toolbox

The NEST simulator is a comprehensive package for the simulation of large neuronal networks, up to tens of thousands of neurons and close to a billion synapses. The simulator is available for most operating systems and allows parallel simulation on multiprocessor computers.

The simulator has been developed in a cooperative effort by the NEST Initiative. For more information and download, please see the NEST Initiative Homepage.

My work on the NEST simulator has been supported by NFR/DAAD through an exchange grant and the eNeuro grant from the Research Council of Norway.

ConnPlotter

ConnPlotter is a tool for visualizing connections in neuronal network models. It is currently compatible with the NEST Topology Module, but should be adaptable to PyNN populations and projections.

The concept behind ConnPlotter is described in the following paper:

E. Nordlie and H. E. Plesser.
Visualizing neuronal network connectivity with connectivity pattern tables.
Front. Neuroinform., 3:39, 2009. Online version.

ConnPlotter Tutorial.

ConnPlotter is provided under the GNU Public License, Version 3, i.e., you are encouraged to use and improve it, as long as you keep it under the GPL. If you do so, please cite our paper and, where appropriate, include a link to this software!

Download

ConnPlotter-0.7.tar.gz (950kB)

ConnPlotter is a Python package. To install it, unpack the archive, move into the ConnPlotter-0.7 directory and run

python setup.py install

ModUhl

The ModUhl collection comprises software for the analysis and simulation of the modulated Ornstein-Uhlenbeck neuron (leaky integrate-and-fire neuron with Gaussian white noise).

I have developed this software as part of my Ph.D. thesis, which is the main source of information on the algorithms contained here. All equation numbers given in the software refer to this thesis:

Hans E. Plesser
Aspects of Signal Processing in Noisy Neurons
Ph.D. thesis, Universität Göttingen, 1999

The software is provided under the GNU Public License, Version 2, i.e., you are encouraged to use and improve it, as long as you keep it under the GPL. If you do so, please cite my thesis and, where appropriate, include a link to this software!

Download

Complete package (gzipped tarball, 1650kB)

Markov Classes

The Markov Classes are a C-library for the efficient simulation of large stochastic dynamic systems. I was originally conceived by Thomas Fricke, and implemented by Dietmar Wendt. I cleaned up the code, wrote a user manual around 1994/5, and added Discrete Classes for system with a small set of fixed rates. Since both of my co-workers from RWTH Aachen have left science, I am currently the only maintainer.

Original Homepage	http://tpd.physik.rwth-aachen.de/papers/classalg.phtml
Download	Complete package (gzipped tarball, 1650kB)

LaTeX & MATLAB Stuff

Below you will find some LaTeX style files and MATLAB scripts that have been useful to me over the past years. Material in the thesis pack is reasonably well tested and documented, while the poster package is very experimental.

Thesis Material	If you want to imitate the layout of my thesis, you'll need this. Includes MATLAB scripts for the figures as well.
Poster Material	LaTeX files that may be useful to create conference posters. Highly experimental.
UMB Beamer Class	I have created a Beamer class for presentations that is (almost) compliant with UMB's new graphical profile. Please contact me if you are interested in this highly experimental piece of software.