bioinformatics

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

Getting Started with Pathomx  data-science

This is quick start-up guide for new users of Pathomx. Following it should give you everything that you need to know to start using Pathomx right away. Once you've been through the basics you might like to see some of the demos to see what Pathomx is capable of ... 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

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

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 (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

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

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