Pathomx For Linux

Pathomx (formerly MetaPath) is an open source graphical software implemented in IPython, Qt and PyQt, designed from the ground up to act as an interactive utility for the visualization and analysis of metabolic data under GNU/Linux and other POSIX operating systems. It was initially engineered to be used for processing metabolomics data.

Key features include support for importing and exporting NMR (Nuclear Magnetic Resonance) data, spectra processing, including normalization, binning and alignment, as well as metabolic pathway visualization and mining. You will also be able to import genomic and metabolomics data through various routes for visualisation on specified pathways.

Various MetaCyc database annotations are also included in the Pathomx application, among which we can mention database unification links, synonyms, as well as associated pathways and reactions. Please note that the MetaCyc database is derived from the public API.

The application uses the powerful MetaCyc database for rapid exploration of complex datasets, thanks to extensible and configurable plugins. It uses the Numpy and Scipy libraries for number handling, Matplotlib for graphing, nmrglue for NMR data import, d3.js for interactive graphs, and scikit-learn for statistical analysis methods.

Looking under the hood of Pathomx, we can notice that the application has been built on IPython command shell. It also works well under Microsoft Windows and Mac OS X operating systems, for which it is available for download as pre-built binary packages. For GNU/Linux, the software is distributed only as a gzipped source archive compatible with 32-bit and 64-bit hardware platforms.

When using Pathomx, users should keep in mind that the application makes use of data from the MetaCyc pathway database itself, which is part of the BioCyc family. The MetaCyc API is used to generate the supplied database, which is stored locally.