Pathomx v3.0.2 released

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.


This latest version adds a number of important features over the previous v2.0 series:

  • IPython backend including a live in-process kernel for debugging and data exploration
  • Pandas dataframe-based data handling
  • Inline code editor: edit the Python code for any tool
  • Figure-based data selection, select regions to exclude from spectra directly on the view output
  • Fully functional python implementation of the icoshift algorithm for NMR (+ other spectra) alignment
  • Support for custom tools, write your own scripts to process your data and connect them up
  • Fixes for PCA and PLS-DA tools, scatter plots to show sample numbers
  • New tools for hierarchical clustering based on Christopher DeBoever's code
  • Improved data importing in both the Text/CSV and Bruker (NMR) tools
  • BioCyc database web API and cached database included
  • Python, MATLAB, R scripting from within Pathomx

The IPython backend gets us all the benefits, bug fixes and improvements from that project directly into Pathomx (currently using the 3.0.0-dev branch). Similarly data handling is now performed (by default) using the Python data analysis library Pandas.



  • Suport for remote cluster processing (to enable jobs to be run on a different computer to that running Pathomx)
  • BioCyc API support for both the web and Pathway Tools API through single interface
  • Improved generic database API to handle management of BioCyc and other data sources
  • More tools, including support for most classification approaches in the sci-kit learn library

Installation and getting started

You can download Pathomx v3.0.2 here. Full documentation is available and there is also a quick getting started guide to teach you the main principles of the software.

Feedback and bug-reports are always welcome.

Continue reading

Pathomx v3.0.0 Release Candidate 2

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! More


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