the things I host on Github

Here are some things related to projects I host at Github.

Currently, these are:


I wrote this to generate documentation for a large set of Perl code I had largely not written myself, and needed to get to grips with. The main ideas of this tool are simple:

I might add support for languages not Perl at some point.


This is an extended version of the one that’s on Sourceforge. It has a couple of new features, including a C++ interface for hybrid MPI/Multithreaded parallel programming.

The main motivation for this project is to be able to

… and still get competitive performance.


This is a set of scripts to help working with models for SASSy, a MATLAB-based software for ODE sensitivity analysis.

The scripts do this:

LineageTracker JSON Export Plugin

LineageTracker is an ImageJ plugin developed by Mike Downey in Till Bretschneider’s group at Warwick University: It can be used to track cell nuclei and extract timeseries from multi-channel images.

This “plugin for a plugin” is useful for exporting data in a format that can be used for automated processing (timeseries analysis, etc.).

Python Template Project

A template Python package with basic Sphinx support (I clone + adapt this when I start new projects).