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SetupX specifications

Information


Unique identifier OMICS_14327
Name SetupX
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
License GNU General Public License version 3.0
Computer skills Advanced
Stability Stable
Maintained Yes

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  • person_outline SetupX Team <>

Publication for SetupX

SetupX in publications

 (20)
PMCID: 5811519
PMID: 29479360
DOI: 10.3389/fpls.2018.00112

[…] metabolites (; , ). recently, a number of databases incorporating ms or nuclear magnetic resonance (nmr)-based metabolomics and statistical tools have been developed, i.e., mery-b, meltdb, and setupx (; ). also, a number of integrated databases (e.g., plantmetabolomics.org) are also emerging (). these include full annotation of metabolites, metabolic profiling and statistical tools. […]

PMCID: 4648992
PMID: 26612985
DOI: 10.1007/s11306-015-0879-3

[…] of articles in the metabolomics journal., more structured (digital) schemata have been proposed, including elaborate xml schema definitions (xsds) or database models like armet (jenkins et al. ) or setupx (scholz and fiehn ), but also lightweight spreadsheet templates (fernie et al. ). a nice summary of community accepted minimal information was presented in a recent editorial (goodacre )., […]

PMCID: 4716583
PMID: 26783503
DOI: 10.1002/psp4.12017

[…] additional information regarding the study design details have been previously published in johnson et al. , study design information was entered into the minix database (a simplified version of the setupx database). all plasma samples were aliquoted and stored at −80°c until use, at which point 30 µl of each sample was thawed, extracted, and derivatized. briefly, 30 µl aliquots were extracted […]

PMCID: 4588804
PMID: 26287255
DOI: 10.3390/metabo5030431

[…] isn’t often effectively leveraged for future experiments. by tracking feature annotations in method and sample specific metabolite atlases this information reused it for experiments; similar to the setupx and binbase system which is widely used in gas-chromatography/mass spectrometry (gc/ms) based metabolomics []. this concept is very simple and essentially makes untargeted experiments behave […]

PMCID: 4615558
PMID: 25531678
DOI: 10.1080/19490976.2014.997612

[…] while 202 lacked full structural identification (unknown metabolites). these unknown metabolites are listed by their binbase identification numbers (http://fiehnlab.ucdavis.edu/projects/binbase_setupx) and the complete dataset is shown in table s1., to characterize the global metabolic differences between groups, a principal component analysis (pca) was applied. serum metabolite profiles […]


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SetupX institution(s)
University of California, Davis Genome Center, CA, USA
SetupX funding source(s)
This work was supported by grant RO1 ES013932 of the NIEHS/National Institutes of Health.

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