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Interactive data analysis built on IPython.

Download v2.5.2
Released 5th May 2014

Available for Windows and MacOS X

About it

Pathomx is a workflow-based tool for the analysis of metabolic pathways and visualisation of associated experimental data. Create workflows, edit and share using the built-in analysis workflow editor. Set up standardised analysis approaches and apply them to new data consistently. Add-remove tools to test different approaches, and re-apply tried and tested methods to new data.

The latest alpha is built on IPython Notebooks allowing construction of workflows from re-useable scripts. Prototype workflows in Pathomx with drag and drop construction and export completed scripts.

For latest updates follow @pathomx on Twitter.

Demos and datasets

We’re making demos of Pathomx in use. If you have a video showing off your own analysis, or demo datasets and workflows you’d like to share send us the link and we’ll list it here.

  1. Monocyte differentiation to macrophage and subsequent polarization (HG-U133B). Demo analysis with a publicly available GEO dataset. Showing import and workflow construction for PCA, PLS-DA and GPML-based pathway visualisation with the visual editor. (Pathomx v2.0.0)
    Download WorkflowGEO datasetGEO metadataGlycolysis WikiPathwayVideo
  2. Demonstrating analysis with the new visual editor showing analysis of multiple datasets, inline views and a number of 1D NMR processing tools.
  3. Short example analysis of 2D metabolomic data showing the advantages of reusing workflows for analysis. Complete preliminary analysis of the dataset in 1m 30s. (Pathomx v1.0.0)

Biology real live analysis

Pathomx started as a metabolomic-analysis platform, and so naturally many of the bundled tools are still geared towards this. The integrated BioCyc database, MetaViz metabolic pathway visualisation tool and support for GPML, WikiPathways, KEGG and more make Pathomx ideal for biological data analysis.

Visualise your data

Visualise your data using matplotlib and d3.js. Generate figures using your own notebooks or the included libomx helpers and then interact with them in the GUI figure editors.

You can save and export figures easily, and manage appearance settings across all figures centrally through the configuration tools.

Open source and free for everyone

Pathomx is available free for any use, licensed under the GPLv3. Helper modules and functions are all released under MIT or BSD licensing and can be shared without restrictions.

Documentation in the know

Documentation is available on Read the Docs. It is a work in progress, if you have the time to help write and test out documentation let us know.

IPython notebook-based tools contain all you need to know to use them simply open up a tool within Pathomx and read away.

Download and get started

Installable binaries are available currently for Mac OS X and Windows.

MSI installer for Windows Vista/7/8 64bit
Disk image (DMG) for Mac OS X (Mountain Lion)

Previous releases are also available for download if required:

The latest developer release is v3.0.0a (IPythonNB) and is available via PyPi or Github. Built versions of the application are available here:

Contribute to make it better

We’re actively looking for Pythonistas to help make Pathomx more awesome. Any level or experience welcome, don’t be shy.

Have a look at the github repository for the open issues tagged “bitesize” or “plugins” for some simple starter tasks. You’re also welcome to take a look at any of the other bugs.

Even easier is contributing IPython Notebooks for custom analysis tools. There isn’t much documentation on this at the moment but check out the bundled tools to see how it all works.

Contact for more info

For more information on Pathomx, development etc. please contact me at:

Martin Fitzpatrick
℅ Centre for Translational Inflammation Research
Queen Elizabeth Hospital
University of Birmingham
United Kingdom
B15 2TT