Writing about software


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 …


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.



IPython notebooks are great for interactively working through analysis problems, so why would you want to automatically run them? To get a record …

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.

from mplstyler import StylesManager
styles = StylesManager …

This short demo shows analysis of a publically available GEO dataset using Pathomx, with a workflow build using the new visual editor (available in the next release).

You can download the example dataset from here.

Pathomx is an open-source workflow-based scientific analysis application. Source code is available here with packaged …


Short demo of an experimental analysis of metabolomic (NMR) data using Pathomx. Metabolomic test dataset produced from THP-1 cells grown under normal and hypoxic conditions. Spectra (2D 1H JRES) have been pre-processed and quantified using the BML-NMR service.

The video shows an example analysis from processed data through to metabolic …

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 …

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


In order to add support for GPML pathways (and later KEGG) in MetaPath I needed a way to get SVG rendered versions of marked up pathways. The …

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