Metabolomics in rheumatology11.09.2015
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 is a workflow-based data analysis tool built on IPython. It began as a metabolomic-analysis toolkit, but has extended to support general data analysis workflows. It aims to be simple to use for non-experts while powerful enough for complex analysis tasks. Key to both of these goals is the ability ...
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
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.
Pathomx v2.5.0 released30.04.2014
Pathomx does MATLAB, R, Python19.02.2014
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 released07.02.2014
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 v2.0.0 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 datasets09.01.2014
MetaPath v1.0.0 released17.12.2013
MetaPath v0.9.9-beta released29.11.2013
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.
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 Analysis13.11.2013
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 ...
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.