Workflow based scientific analysis built on Python
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Latest stable release v3.0.2 (24th October 2014).

Pathomx is an interactive tool for the analysis and visualisation of scientific data. Built on IPython it allows rapid, workflow-based exploration of complex datasets through configurable tool-scripts. Originally designed for the processing of metabolomics data it can equally be applied to the analysis of other biological or scientific data.

Metabolomics-specific tools include NMR data import and export, spectra processing inc. normalisation, alignment, and binning, and metabolic pathway mining and visualisation. It ships with set of the the MetaCyc database derived from the public API containing most key metabolic pathways. Annotations from the MetaCyc database are available including synonyms, associated reactions and pathways and database unification links.

Stable The current trunk of Pathomx is stable and can be built using cx_Freeze (as-is on Windows, with some tweaks on Mac). The latest version (3.0.0) is now available to download Windows 7 & 8 (x64)Mac OS X Mountain Lion .appGithub


It is developed in Python, using Qt5/PyQt5, Matplotlib (for graphing), numpy/scipy (for number handling), nmrglue (for NMR data import), scikit-learn (for statistical analysis methods).

Download Windows 7 & 8 (x64)Mac OS X Mountain Lion .appGithub

Pathomx requires installation of Graphviz for pathway drawing.


Pathomx is available free for any use under the GPLv3 license.

Pathomx uses data from the MetaCyc pathway database itself part of the BioCyc family. The supplied database is generated via the MetaCyc API and stored locally. Licenses for the entire MetaCyc database are also available free of charge for academic and government use.