Toward collaborative open data science in metabolomics using Jupyter Notebooks and cloud computing

[1] Afgan E(2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Nucleic Acids Research 46 W537-W544

[2] Baker D(2016)1,500 scientists lift the lid on reproducibility Nature 533 452-454

[3] Batut B(2018)Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies Metabolomics 14 72-196

[4] van den Beek M(2006)Statistical strategies for avoiding false discoveries in metabolomics and related experiments Metabolomics 2 171-62

[5] Bouvier D(2016)(1)H-NMR urinary metabolomic profiling for diagnosis of gastric cancer British Journal of Cancer 114 59-S68

[6] Cech M(2017)Critical review of reporting of the data analysis step in metabolomics Metabolomics 14 7-1495

[7] Chilton J(2016)Galaxy-M: A Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data GigaScience 5 10-241

[8] Clements D(2010)Visualization of omics data for systems biology Nature Methods 7 S56-D786

[9] Coraor N(2015)Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics Bioinformatics (Oxford, England) 31 1493-748

[10] Gruning BA(2007)Proposed minimum reporting standards for data analysis in metabolomics Metabolomics 3 231-714

[1] Afgan E(2018)The Galaxy platform for accessible, reproducible and collaborative biomedical analyses: 2018 update Nucleic Acids Research 46 W537-W544

[2] Baker D(2016)1,500 scientists lift the lid on reproducibility Nature 533 452-454

[3] Batut B(2018)Guidelines and considerations for the use of system suitability and quality control samples in mass spectrometry assays applied in untargeted clinical metabolomic studies Metabolomics 14 72-196

[4] van den Beek M(2006)Statistical strategies for avoiding false discoveries in metabolomics and related experiments Metabolomics 2 171-62

[5] Bouvier D(2016)(1)H-NMR urinary metabolomic profiling for diagnosis of gastric cancer British Journal of Cancer 114 59-S68

[6] Cech M(2017)Critical review of reporting of the data analysis step in metabolomics Metabolomics 14 7-1495

[7] Chilton J(2016)Galaxy-M: A Galaxy workflow for processing and analyzing direct infusion and liquid chromatography mass spectrometry-based metabolomics data GigaScience 5 10-241

[8] Clements D(2010)Visualization of omics data for systems biology Nature Methods 7 S56-D786

[9] Coraor N(2015)Workflow4Metabolomics: A collaborative research infrastructure for computational metabolomics Bioinformatics (Oxford, England) 31 1493-748

[10] Gruning BA(2007)Proposed minimum reporting standards for data analysis in metabolomics Metabolomics 3 231-714