About

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.

Latest

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.

Screenshot

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.

MetaPath is now Pathomx

MetaPath has now been renamed Pathomx. The name change was neccessary due to a name clash with another piece of published bioinformatics software, but it also better reflects the focus on analysis of multi-omics data in a pathway context.

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Projects

Accuri2FCS

Convert Accuri .c6 files to .fcs standard

BioCyc

Python interface to the BioCyc Web API

GPML2SVG

A command-line/Python GPML to SVG pathway renderer

Icoshift (Python)

A Python implmentation of the Icoshift algorithm

mplstyler

An API for assigning consistent marker styles to Matplotlib plots.

The Open Lab Book

Freely available lab protocols under a CC license

MetaboHunter

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

Pathminer

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

Pathomx

Workflow-based metabolomic analysis tool

PyQtConfig

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

QtIPy

IPython Notebook automator