bioinformatics

Pathomx Linux Developer Release04.01.2015

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 ...


Getting Started with Pathomx08.12.2014

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 ...



Pathomx v3.0.2 released26.10.2014

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.


Pathomx v3.0.0 Release Candidate 207.10.2014

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!


Pathomx v3.0.0alpha4 for Mac15.07.2014

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.



MetaboHunter (API)25.05.2014

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.


BioCyc (API)24.05.2014

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.


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Pathomx (née MetaPath) v2.2.0 released07.02.2014

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.


MetaPath is now Pathomx04.02.2014

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.


MetaPath v2: Visual analysis for metabolomics [Released]13.01.2014

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.


Cytoscape v3.0.2 on Mac OS X08.08.2013

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 ...


MetaPath v0.7.0 Released03.07.2013

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.


MetaPath v0.6.0 Released20.06.2013

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.


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