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Protocols

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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Publication for SetupX

SetupX citations

 (23)
library_books

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

2018
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., plantmetabolomics.org) are also emerging (). These include full annotation of metabolites, metabolic profiling and statistical tools. This in […]

library_books

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

2016
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 […]

library_books

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

2015
Metabolomics
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 […]

library_books

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

2015
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 […]

library_books

Analysis of Metabolomics Datasets with High Performance Computing and Metabolite Atlases

2015
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 […]

library_books

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

2015
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 (http://fiehnlab.ucdavis.edu/projects/binbase_setupx) 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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