software

Wooey

Wooey

Pathomx Linux Developer Release 04.01.2015

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 ...


PyQtConfig

PyQtConfig

Pathomx v3.0.2 released 26.10.2014

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 2 07.10.2014

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 Mac 15.07.2014

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.



QtIPy

QtIPy

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Pathomx does MATLAB, R, Python 19.02.2014

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 ...


Pathomx (née MetaPath) v2.2.0 released 07.02.2014

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 Pathomx 04.02.2014

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.


Pathomx: Analysis of public GEO datasets 09.01.2014

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).


MetaPath v1.0.0 released 17.12.2013

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.


MetaPath v0.9.9-beta released 29.11.2013

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.


NCBI Gene Expression Omnibus (GEO) support added to MetaPath 18.11.2013

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 ...


Pathomx: Example Analysis 13.11.2013

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 ...



MetaPath gets flexible: An interactive analysis workflow tool 13.10.2013

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.


MetaPath v0.7.0 Released 03.07.2013

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 Released 20.06.2013

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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