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

Dataset type: Metabolomic, Software, Workflow, Virtual-Machine
Data released on December 22, 2015

Davidson RL; Liu H; Sharma-Oates A; Viant MR; Weber RJM (2015): Supporting material for "Galaxy-M: A galaxy workflow for processing and analysing direct infusion and liquid chromatography mass spectrometry-based metabolomics data". GigaScience Database. http://dx.doi.org/10.5524/100146

DOI10.5524/100146

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.
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).
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.
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.

*****Please note*****
It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server.
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.

Additional details

Read the peer-reviewed publication(s):

Davidson, R. L., Weber, R. J. M., Liu, H., Sharma-Oates, A., & Viant, M. R. (2016). Galaxy-M: a Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data. GigaScience, 5(1). doi:10.1186/s13742-016-0115-8

Related datasets:

doi:10.5524/100146 References doi:10.5524/100108

Additional information:

https://github.com/Viant-Metabolomics/Galaxy-M

https://github.com/Viant-Metabolomics/MI-Pack

Accessions (data included in GigaDB):

MetaboLights: MTBLS146
MetaboLights: MTBLS79





Sample IDTaxonomic IDCommon NameGenbank NameScientific NameSample Attributes
batch01_C19913bovinecattleBos taurus Description:example data produced as part of the metabolights accession MTBLS79
batch01_C109913bovinecattleBos taurus Description:example data produced as part of the metabolights accession MTBLS79
batch01_QC-1None assignedNone assignedNone assigned Description:the instrument blank sample
batch01_S19940SheepsheepOvis aries Description:example data produced as part of the metabolights accession MTBLS79
batch01_S79940SheepsheepOvis aries Description:example data produced as part of the metabolights accession MTBLS79
batch04_B-1None assignedNone assignedNone assigned Description:the reagent blank sample
PDP12AE00291-49606HumanhumanHomo sapiens Age:25
Alternative names:F01
Body product:blood plasma
...
+
PDP12AJ02668-49606HumanhumanHomo sapiens Age:21
Alternative names:F03
Body product:blood plasma
...
+
PDP12AJ02988-49606HumanhumanHomo sapiens Age:23
Alternative names:F06
Body product:blood plasma
...
+
PDP12AJ03026-49606HumanhumanHomo sapiens Age:32
Alternative names:F07
Body product:blood plasma
...
+
Displaying 1-10 of 21 Sample(s).




File NameSample IDData TypeFile FormatSizeRelease Date 
PDP12AE00291-4Mass Spectrometry datamzML30.32 MB2015-08-26
PDP12AJ02668-4Mass Spectrometry datamzML30.55 MB2015-08-26
PDP12AJ02988-4Mass Spectrometry datamzML30.52 MB2015-08-26
PDP12AR02407-4Mass Spectrometry datamzML30.32 MB2015-08-26
PDP12AR02412-4Mass Spectrometry datamzML30.17 MB2015-08-26
PDP12AR02422-4Mass Spectrometry datamzML30.24 MB2015-08-26
PDP12AR02435-4Mass Spectrometry datamzML30.21 MB2015-08-26
PDP12AR02500-4Mass Spectrometry datamzML30.46 MB2015-08-26
PDP12AR02554-4Mass Spectrometry datamzML30.39 MB2015-08-26
PDP12AR02624-4Mass Spectrometry datamzML30.46 MB2015-08-26
Displaying 1-10 of 1891 File(s).
Funding body Awardee Award ID Comments
Research Councils UK NE/K011294/1 Mark Viant & Rob L Davidson
Research Councils UK R8-H10-61 Mark Viant
Date Action
December 22, 2015 Dataset publish
May 6, 2016 Description updated from : 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.
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).
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.
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.
May 6, 2016 Description updated from : 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.
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).
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.
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.

*****Please note***** It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server.
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.
May 6, 2016 Description updated from : 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.
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).
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.
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.

span { font-family: arial, 'times new roman'; color: #f00; *****Please note*****
It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server.
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. }
June 13, 2016 Manuscript Link added : 10.1186/s13742-016-0115-8
June 24, 2016 Description updated from : 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.
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).
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.
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.

*****Please note*****
It has been reported that there is a problem with the file "Virtual Machine.zip", so we have removed it from our server.
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.