Since about 2016 my group has been posting all code (and data when needed) necessary to reproduce the results in our papers on Github. The links to the repositories can be
found in the manuscripts. The following includes links to older files.

A Model of the VS Network of the Blowfly

James Trousdale and Sam Carroll developed some code that we obtained from Alexander Borst and Yishai Elyada. You can find the code along with instructions on how to use it here.

Neuronal Network Simulations and Linear Response Approximation to the Resulting Cross-Correlations

This folder contains the code to simulate a network of EIF neurons. It also includes code that computes the linear response kernels for the cells in the network. The correlations between the cells in the network are computed both from simulations, and approximated using the linear response properties. Instructions are provided here, and a full description of the problem and the methods can be found in this paper.

Generation of Spatio-Temporally Correlated Spike Trains

This code allows for the generation of spike trains with predefined temporal cross-correlation functions. It accompanies this paper.

Stochastic Integrate-and-Fire Neurons

An implementatioin of the finite volume method for the solution of the Fokker-Planck equation described in the article with F. Marpeau and A. Barua is available at SourceForge.

We have also extended the code to model two, potentially coupled neurons. The code is available here, and the accompanying documentation can be found here.

Imaging of Ripples in Neural Tissue

Matlab code for the spatiotemporal patterns obtained using voltage sensitive dyes is available here. Documentation is available here.

Nonautonomous Differential Equations

You can find animations and Mathematica files that accompany my article with Robert Rosenbaum on nonautomous differential equations here.