Supporting material for "Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data".

Metabolomics is increasingly recognised as an invaluable tool in the biological, medical and environmental sciences yet lags behind the methodological maturity of other omics fields, specifically genomics and transcriptomics. To achieve its full potential, including the integration of multiple omics modalities, the accessibility, standardisation and reproducibility of computational metabolomics tools must to be improved significantly.<br>Here we present an end-to-end metabolomics analysis pipeline that has been developed for both direct infusion mass spectrometry (DIMS) and liquid chromatography mass spectrometry (LC-MS) metabolomics, all wrapped in the Galaxy workflow system. This data repository provides the software and Galaxy configuration files alongside two small test datasets (1xFT-ICR DIMS, 1xLC-MS). <br>To further aid accessibility, the tools, Galaxy and example data are all provided pre-installed in a virtual machine (Ubuntu 14.04LTS 64bit, in the OVF format) that can be downloaded from this repository. <br>Additionally, source code, executables and installation instructions are available from Github and users are encouraged to check this for the most recent updates and additions.<br><br> *****Please note*****<br> It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server. <br> We are currently in discussion with the authors to try to rectify this problem. This notice will be removed when we have a working version of the file available. Sorry for any inconvenience.