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W4M specifications

Information


Unique identifier OMICS_23162
Name W4M
Alternative name Workflow4Metabolomics
Software type Pipeline/Workflow
Interface Web user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 3.0
Computer skills Basic
Version 3.0
Stability Stable
Maintained Yes

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Publications for Workflow4Metabolomics

W4M in publications

 (7)
PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] these include: metaboanalyst (xia et al. , ; xia and wishart ) for multivariate analysis, metabolite annotation and biological interpretation, mvapack for multivariate analysis (worley and powers ), workflow4metabolomics for multivariate analysis (giacomoni et al. ), metassimulo for multivariate analysis (muncey et al. ), the human metabolome database (hmdb) for metabolite annotation […]

PMCID: 5852740
PMID: 29385065
DOI: 10.3390/nu10020164

[…] were initially preprocessed with xcalibur 2.2® (thermo fisher scientific, san jose, ca, usa), converted to the (*.mzxml) cross-platform open file format, using msconvert® [], and processed using workflow4metabolomics® (w4m) (http://workflow4metabolomics.org) []. lipidomic data were extracted using: (i) pre-processing with the open-source xcms® [] within w4m [], for nonlinear retention time […]

PMCID: 5627583
PMID: 29043062
DOI: 10.5256/f1000research.13363.r25758

[…] the curated data (spectra, compounds, networks) and workflows will be of high value as input for the corresponding reference repositories and e-infrastructures (metabolights, chebi, metexplore, workflow4metabolomics, phenomenal)., europe is a major provider of massive and high-quality metabolomics data. large endeavors such as the mrc-nihr national phenome centre ( […]

PMCID: 5333891
PMID: 28253346
DOI: 10.1371/journal.pone.0173315

[…] the mobile phase (0.2% acetic acid in water–acetonitrile) was programmed from 95: 5 to 5: 95 acetonitrile–water (v: v)., mass spectra data were processed by xcms using the online version of galaxy-workflow4metabolomics [], after conversion of raw spectra to mzxml format. data processing was performed using centwave method for the peak picking, with a maximum deviation of 4 ppm. […]

PMCID: 4754433
PMID: 26909353
DOI: 10.3389/fmolb.2016.00002

[…] in the scope of current efforts of the metabolomics community to create data analysis pipelines implemented in generic frameworks like galaxy. for instance, this approach will be integrated in the workflow4metabolomics developed by metabohub (giacomoni et al., )., the proposed pipeline is a simplified way to map an entire chemical library on a large range of organism-specific metabolic […]


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W4M institution(s)
INRA, UMR 1019, PFEM, Saint Genes Champanelle, France; CNRS, UPMC, FR2424, ABiMS, Station Biologique, Roscoff, France; INRA, UMR 1331, PF MetaToul-AXIOM, Toxalim, Toulouse, France; INRA, Metabolome Facility of Bordeaux Functional Genomics Center, IBVM, Villenave d’Ornon, France; CEA, LIST, Laboratory for Data Analysis and Smart Systems (LADIS), MetaboHUB Paris, Gif-sur-Yvette, France
W4M funding source(s)
Supported by Biogenouest, Lifegrid (Auvergne), and by the IDEALG project [ANR-10-BTBR-04], IFB [ANR-11- INBS-0013] and MetaboHUB [ANR-11-INBS-0010] grants.

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