Open Source

Wooey  web

Wooey is a simple web interface to run command line Python scripts. Think of it as an easy way to get your scripts up on the web for routine data analysis, file processing, or anything else. The project was inspired by how simply and powerfully sandman could expose users to ... More


PyQtConfig: a simple API for handling, persisting and synchronising configuration within PyQt applications. This module was built initially as part of the Pathomx data analysis platform but spun out into a standalone module when it became clear it was quite useful. More

MetaboHunter (API)

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

BioCyc (API)

BioCyc is a Python 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. More


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. More


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. More


Pathomx is a unique workflow-based analysis tool that provides complete analytical control while maximising usability. Construct complex analysis workflows including multivariate, univariate and pathway-mining approaches from a simple drag-drop interface. Configure tools and immediately see the result reflected downstream. Prototype scripts and share or export the result for others to ... More


A Python implementation of the Icoshift algorithm, a versatile tool for the rapid alignment of 1D NMR spectra More


A command line program for the conversion of Accuri .c6 flow cytometry data files to the standard .fcs format, has been released today via github and PyPi. More


Gpml2svg, a command-line/Python API for rendering GPML (GenMAPP Pathway Markup Language) to SVG, has been released today via github and PyPi. More