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SetupX specifications


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




No version available


  • person_outline SetupX Team

Publication for SetupX

SetupX citations


The Chemistry of Plant–Microbe Interactions in the Rhizosphere and the Potential for Metabolomics to Reveal Signaling Related to Defense Priming and Induced Systemic Resistance

Front Plant Sci
PMCID: 5811519
PMID: 29479360
DOI: 10.3389/fpls.2018.00112

[…] tified 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., are also emerging (). These include full annotation of metabolites, metabolic profiling and statistical tools. This in […]


Metabolomic signatures of drug response phenotypes for ketamine and esketamine in subjects with refractory major depressive disorder: new mechanistic insights for rapid acting antidepressants

PMCID: 5048196
PMID: 27648916
DOI: 10.1038/tp.2016.145

[…] GC-TOF—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. All metabolites were measured as peak hei […]


Data standards can boost metabolomics research, and if there is a will, there is a way

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

[…] 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 ).Althou […]


Pharmacometabolomic Assessments of Atenolol and Hydrochlorothiazide Treatment Reveal Novel Drug Response Phenotypes

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

[…] 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 wi […]


Analysis of Metabolomics Datasets with High Performance Computing and Metabolite Atlases

PMCID: 4588804
PMID: 26287255
DOI: 10.3390/metabo5030431

[…] n 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 mo […]


Alteration of the fecal microbiota and serum metabolite profiles in dogs with idiopathic inflammatory bowel disease

PMCID: 4615558
PMID: 25531678
DOI: 10.1080/19490976.2014.997612

[…] ites, while 202 lacked full structural identification (unknown metabolites). These unknown metabolites are listed by their Binbase identification numbers ( and the complete dataset is shown in Table S1. […]

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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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