MetaboFlow aims at building, testing and delivering cloud-based Galaxy workflow(s), with the computational capacity to process datasets with 1000s of samples and simultaneously capture all metadata associated to allow rigorous reproducibility and reporting.

MetaboFlow infrastructure is formulated based on several community-agreed popular processing, feature extraction, compound identification tools and necessary functionality is incorporated to readily use online metabolomics databases such as MetaboLights.



We develop online tools for complete analysis of metabolomic data, from its acquisition through to novel statistical/machine learning methods used to process data, and spectral tools used to annotate the mass and NMR spectra.

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New algorithms/tools and existing tools are wrapped into Galaxy for processing and analysing metabolomics data as well as for compound identification. This enables us not only to addresses the bottlenecks in the workflow but also extend the pipeline functionality.

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Improvements in reproducibility in analytical equipment, individual laboratories are acquiring larger, more complex datasets, which are a significant challenge to process.Metabolomics lacks reproducible computational workflows based on internationally accepted standard operating procedures and this is impacting on the field in terms of reproducibility of studies and subsequent sharing of data. We aim to develop a Galaxy workflow(s) for the processing of metabolomic and lipidomic data including the most widely used open source tools, aiding reproducibility and transferability of metabolomic data.


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To address the community need(s) we have conducted an online survey (MetaboNews and the Metabolomics Society) of computational tools used by the metabolomics community. Our strategy, mainly based on the outcome of this survey is to develop workflows by using tools that are already widely used in metabolomics, allowing us greater resources to develop new tools where popular open source tools have not been developed (e.g. imaging with metabolomics).


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Biomedical Resource and Technology Development Grant | 202952

MetaboFlow - the development of standardised workflows for processing metabolomics data to aid reproducible data sharing and big data initiatives

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