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

Icoshift

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

Cytoscape v3.0.2 on Mac OS X  science

Cytoscape 3.0.2 was released on 1st August, a bugfix release for the 3.x series. However, there is a compatibility issue with the latest Java update from Apple resulting in Cytoscape hanging on startup. I'd followed advice found elsewhere to update to the latest Java version with ... 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

accuri2fcs

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

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

cx_Freeze and PySide on Mac  gui

I'd had success using py2app for building Mac binaries for distribution but wanted to give cx_Freeze a go since it's cross platform - allowing builds for Windows, Linux, and more. Unfortunately, attempting to build using cx_Freeze was resulting in errors: libpyside-python2.7.1.1.dylib: No such file or ... More

Pelicans on Webfaction  web

As mentioned in the previous post, I recently migrated this site over to the very clever Pelican. Setting it up was relatively straightforward using a combination of the official docs, this post and linked github repo from Dominic Rodger. That said, there were a few things that I stumbled at and non-obvious decisions that I've documented below. More

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