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

BMC Bioinformatics. 2014 Dec 10;15(1):396. doi: 10.1186/s12859-014-0396-9.

Abstract

Background: 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.

Results: 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 (1)H NMR metabolomic data from a model system of mammalian cell growth under hypoxic conditions.

Conclusions: 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.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Cells, Cultured
  • Computational Biology / methods*
  • Databases, Factual*
  • Humans
  • Macrophages / cytology
  • Macrophages / metabolism*
  • Magnetic Resonance Spectroscopy
  • Metabolic Networks and Pathways
  • Metabolomics / methods*
  • Reproducibility of Results
  • Software*
  • Workflow*