I am a final-year PhD student working on the metabolomics of inflammatory diseases.
On this site you’ll find details of my publications and software, together with articles relating to how to make use of one or the other.
Everything you see here is licensed CC-BY-SA and GPLv3.


Pathomx v3.0.0 Release Candidate 2

The final release candidate for Pathomx v3.0.0 is available for both Mac and Windows. This latest version features the new IPython backend providing parallel processing (via IPython ipcluster support), numerous bugfixes and improvements to the UI and figure outputs. While a development version it is considered stable enough for regular use.

If you’re a current user of Pathomx, please download and test with your own hardware and data, see how it holds up and then report any problems!

Pathomx v3.0.0alpha4 for Mac

A development version of Pathomx v3.0.0-alpha4 is now available as a installable app for Mac. This latest version showcases the new IPython backend, with notebooks and reports.

PyQt5 support in Matplotlib

My pull-request for matplotlib to add PyQt5 support has been accepted and merged, meaning PyQt5 support will be available in the upcoming v1.4.0 release of matplotlib.

Pathomx meets IPython - Workflow construction with IPython notebooks (and vice versa)

A new developer release of Pathomx (v3.0.0a) is out today via Github and PyPi. This release brings an IPython backend and support for IPython-notebook based plugins.

MetaboHunter from Python: 1D NMR Metabolite Identification

Another Python module released today. MetaboHunter is a Python module for accessing the MetaboHunter web service for automated assignment of 1D raw, bucketed or peak picked NMR spectra.

BioCyc Web API for Python

Today I’ve released Python module BioCyc that provides an interface to the BioCyc Web API. Acting as a wrapper it queries the database and then presents the XML returned in a pythonic object-based interface. Support for IPython views is included offering nice summary tables of object attributes.

QtIPy: The data automator!

Today sees the release of a little utility: QtIPy: The data automator! a simple GUI-based run-automator for IPython notebooks. It allows you to attach triggers to files, folders or timers to automatically run notebooks.

mplstyler: A simple API to keep line and marker styles consistent throughout plots

I’ve just released a simple API for managing matplotlib line and marker styles for plots. It’s called mplstyler and you can get it from Github or PyPi. This code is based on the style manager in Pathomx, extracted for more general use.

Pathomx v2.5.0 released

Pathomx v2.5.0 has been released for both Windows and MacOS X.

QColorButton: A color-selector tool for PyQt

Below is a short snippet to implement a color-picker attached to a button in Qt. Clicking on the button pops up a dialog (native) to select a color. The color is shown by the color of the button face. A right-click option is included to allow clearing of the color ...

Pathomx does MATLAB, R, Python

The development version of Pathomx now supports custom scripting in Python, MATLAB and R.


Integration with existing omics workflows is a key goal of Pathomx, and to do this requires interoperability with other platforms. In the upcoming release you’ll now get access to custom scripting in MATLAB, R or ...

Pathomx (née MetaPath) v2.2.0 released

MetaPath is now named Pathomx, reflecting the focus on analysis of multi-omics data within pathway contexts. Pathomx v2.2.0 has also been released for both Windows and MacOS X.

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Convert Accuri .c6 files to .fcs standard


Python interface to the BioCyc Web API


A command-line/Python GPML to SVG pathway renderer

Icoshift (Python)

A Python implmentation of the Icoshift algorithm


An API for assigning consistent marker styles to Matplotlib plots.

The Open Lab Book

Freely available lab protocols under a CC license


A Python interface to the MetaboHunter 1D NMR metabolite identification service


Algorithmically score and select pathways/reactions from compound, protein or gene data


Workflow-based metabolomic analysis tool


A PyQt config manager. Keep Qt widgets in sync with a config dictionary and/or QSettings object.


IPython Notebook automator