Pathomx: an interactive workflow-based tool for the analysis of metabolomic data

Martin A Fitzpatrick, Catherine M McGrath, Stephen P Young

Research output: Contribution to journalArticlepeer-review

18 Citations (Scopus)
311 Downloads (Pure)



Metabolomics is a systems approach to the analysis of cellular processes through small-molecule metabolite profiling. Standardisation of sample handling and acquisition approaches has contributed to reproducibility. However, the development of robust methods for the analysis of metabolomic data is a work-in-progress. The tools that do exist are often not well integrated, requiring manual data handling and custom scripting on a case-by-case basis. Furthermore, existing tools often require experience with programming environments such as MATLAB® or R to use, limiting accessibility. Here we present Pathomx, a workflow-based tool for the processing, analysis and visualisation of metabolomic and associated data in an intuitive and extensible environment.


The core application provides a workflow editor, IPython kernel and a HumanCyc™-derived database of metabolites, proteins and genes. Toolkits provide reusable tools that may be linked together to create complex workflows. Pathomx is released with a base set of plugins for the import, processing and visualisation of data. The IPython backend provides integration with existing platforms including MATLAB® and R, allowing data to be seamlessly transferred. Pathomx is supplied with a series of demonstration workflows and datasets. To demonstrate the use of the software we here present an analysis of 1D and 2D 1H NMR metabolomic data from a model system of mammalian cell growth under hypoxic conditions.


Pathomx is a useful addition to the analysis toolbox. The intuitive interface lowers the barrier to entry for non-experts, while scriptable tools and integration with existing tools supports complex analysis. We welcome contributions from the community.

Original languageEnglish
Article number396
Number of pages7
JournalBMC Bioinformatics
Issue number1
Publication statusPublished - 10 Dec 2014


  • Metabolomics
  • Omics
  • nmr
  • Analysis
  • Visualisation
  • Workflow
  • Automation
  • Python


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