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Rapid workflow-based metabolomic analysis

Free and open source GPLv3

Available for Windows and MacOSX
Latest version v2.4 released on 18th April 2014


Pathomx is a workflow-based tool for the analysis of metabolomic and other omics datasets. It is interactive, visual, extensible, intelligent and free for any use.


Dynamically build analysis workflows using the interactive editor. Drag and drop connections between plugin tools to create a complete workflow through which to run your analysis. Data can be loaded and processed automatically, and new approaches tested by simply connecting up tools.

Pathomx visualisation example


Data visualisation is key to the analysis of complex datasets. Pathomx is supplied with a range of standard and novel visualisation plugins, allowing exploration of data in new and useful ways.

Pathomx visualisation example


Pathomx is built on the MetaCyc database, allowing seamless mapping of experimental data to real biological entities. Follow interactions, reactions and pathways to understand data in the biological context. Multiple annotations from the MetaCyc database are available including synonyms, associated reactions and pathways and database unification links. Additionally the database includes links to the online MetaCyc database and to other related resources including KEGG, PubChem, CAS, CHEBI and KNApSAcK.

Pathomx internal MetaCyc database


Workflow capabilities are managed through analysis plugins, which can be added and removed at will. Already Pathomx supports a range of different data import, processing and visualisation options for various types of data. Support for interaction with other systems including MATLAB and R is in development, and we welcome contributions of plugins from the community.

Pathomx visualisation example

Free & Open Source

Pathomx is available for free for any use, licensed under the GPLv3. This means you are free to download, install, copy and share this software with absolutely anyone you like.

If you are technically minded the source code is also available and we gladly welcome contributions from other scientists, developers, academics or general users.

Pathomx is built on the MetaCyc pathway database itself part of the BioCyc and HumanCyc family. The supplied database is generated via the MetaCyc API and stored locally. Licenses for the entire MetaCyc database are also available free of charge for academic and government use.

Molecular structures are derived from the KEGG database, developed by Kanehisa Laboratories. If using molecular structure annotations please cite the following article(s): Kanehisa, M. and Goto, S.; KEGG: Kyoto Encyclopedia of Genes and Genomes. Nucleic Acids Res. 28, 27-30 (2000).

Want more?

You can download Pathomx, get more information, watch demos or explore plugins.

Pathomx is under continued development. If you spot bugs, or have suggestions for improvement, please submit them via our github bug tracker. We welcome community input of code, plugins, d3 graphs and other contributions.