A simulator for spiking neural networks. It is written in Python for rapid development and ease-of-use, and generates code in several different languages for a variety of computational devices for efficient execution (for example on GPU via the GeNN simulator using the Brian2GeNN package). It includes packages for automatically fitting neuron models to experimental data and for modelling the auditory system.
A collection of programs for "spike sorting". That is, for extracting spike trains from a set of simultaneously recorded extracellular traces. This problem involves preprocessing data to remove noise, clustering to identify patterns across channels that correspond to spikes, and finally manually inspecting and refining the output. This software is currently undergoing a massive redesign to make it possible to sort spikes using enormous electrode arrays with hundreds to thousands of channels.
The KlustaSuite team is led by Kenneth Harris at UCL.
A package for graph layout based on a stochastic gradient descent algorithm (available for C++ and Python). The package is described in the paper Graph Drawing by Stochastic Gradient Descent (Zheng et al. 2018) and was written by Jonny Zheng.
A game for exploring the development and maintenance of ecosystems for both education and research purposes. The game was written by Jonathan Zheng, with ecosystems modelling by Orestes Gutierrez and Samraat Pawar.
Software for power-confluent drawings, accompanying the paper Further Towards Unambiguous Edge Bundling: Investigating Power-Confluent Drawings for Network Visualization (Zheng et al. 2019) written by Jonny Zheng.