software

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

Pathomx Linux Developer Release

A developer release of Pathomx (Python3) is now available. This release can be installed by using the ./developer_release_linux_python3.sh script from the cloned Github repository. This script installs all dependencies (via apt-get and pip) that are required for Pathomx to run. This developer release is an important first step to ... More

PyQtConfig

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

Pathomx v3.0.2 released

Pathomx v3.0.2 has been released for both Windows and MacOS X. This marks the first stable, bug-fixed release for the v3.0 line featuring the new IPython-kernel with cluster support for parallel processing of tools. More

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! More

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. More

QtIPy

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

mplstyler

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 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 ... More

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. More

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. More

MetaPath v2: Visual analysis for metabolomics [Released]

MetaPath v2.0.0 has been released today! This latest version features a new visual editor for construction fo analysis workflows, new analysis plugins, graphing powered by Matplotlib and all sorts of other goodness. Downloads are available for Windows and MacOS X. More

MetaPath v1.0.0 released

MetaPath v1.0.0 has been released today for both Windows and MacOS X. In addition, MetaPath now has its own website for updates, demos, plugins and more. More

MetaPath v0.9.9-beta released

An up-to-date build of MetaPath for Mac OS X is available for download today. This is the first public build supporting the interactive workflow, automated processing, NMR spectra processing, gene expression analysis, PCA, PLS-DA, and the rest. More

NCBI Gene Expression Omnibus (GEO) support added to MetaPath

The NCBI Gene Expression Omnibus (GEO) is 'is a public functional genomics data repository supporting MIAME-compliant data submissions.' In other words, its a online database of freely available experimental gene-expression data. Quite useful. To make this resource available to users of MetaPath I've today released a simple GEO-data import ... More

Pathomx: Example Analysis  science

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 ... More

Pathomx

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

MetaPath gets flexible: An interactive analysis workflow tool

It's been a while since I've posted an update on MetaPath development, which is finally forming into a solid package ready for publication. The latest version is available here on Github, with binary packages to follow in the near future. It's quite a transformation from earlier versions, so I thougth I'd take some time to walk through the new features and ideas, with a few notes on implementation. More

MetaPath v0.7.0 Released

An update has been released today for MetaPath, a metabolic pathway visualisation and analysis tool. It is available via PyPi and github. A Mac .app bundle is also available. More

MetaPath v0.6.0 Released

An update has been released today for MetaPath, a metabolic pathway visualisation and analysis tool. It is available via PyPi and github. A Mac .app bundle is also available. More

gpml2svg

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