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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.

This post first appeared on Martin Fitzpatrick – Python Coder, Postgraduate, please read the originial post: here

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Pathomx v3.0.2 released


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