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
Feedback and bug-reports are always welcome.