Projects per year
Abstract
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.
ResultsThe 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.
ConclusionsPathomx 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 language | English |
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Article number | 396 |
Number of pages | 7 |
Journal | BMC Bioinformatics |
Volume | 15 |
Issue number | 1 |
DOIs | |
Publication status | Published - 10 Dec 2014 |
Keywords
- Metabolomics
- Omics
- nmr
- Analysis
- Visualisation
- Workflow
- Automation
- Python
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Dive into the research topics of 'Pathomx: an interactive workflow-based tool for the analysis of metabolomic data'. Together they form a unique fingerprint.Projects
- 2 Finished
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Centre for Musculoskeletal Ageing Research (linked to 18289 & 19482)
Lord, J., Buckley, C., Duda, J., Dunn, W., Miall, C. & Greig, C.
1/08/12 → 31/07/17
Project: Research Councils
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Wellcome Trust combined training programme - M Fitzpatrick
Young, S. & Gordon, J.
1/10/10 → 30/09/14
Project: Research