Automics protocols

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Automics specifications

Information


Unique identifier OMICS_02837
Name Automics
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Windows
Programming languages C++
License GNU General Public License version 2.0
Computer skills Advanced
Stability Stable
Maintained Yes

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Maintainers


  • person_outline Bin Xia <>
  • person_outline Kang Shao <>
  • person_outline Qinying Chu <>
  • person_outline Yanfei Ren <>

Publication for Automics

Automics in pipelines

 (2)
2018
PMCID: 5809546
PMID: 29479299
DOI: 10.1007/s11306-018-1321-4

[…] spike-in methods or peak look-up tables (martinez-arranz et al. ). a variety of software packages for nmr statistical spectroscopy have been developed including, metassimulo (muncey et al. ), automics (wang et al. ), statistical total correlation spectroscopy (cloarec et al. , ), and mvapack (worley and powers )., for relatively simple biofluids such as serum, plasma, cerebrospinal fluid […]

2016
PMCID: 4876396
PMID: 27212081
DOI: 10.1038/srep26515

[…] d baseline corrected and calibrated using the internal standard (dss-d6)., phased and baseline-corrected 1h nmr spectra were binned from 8.0 to 0.5 ppm with a bin width of 0.02 ppm using the software automics. binning was performed applying the total scaling function of automics and the region from 5.0 to 4.6 ppm (hdo signal) was not binned. the matrix with the data of all the binned spectra (355  […]


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Automics in publications

 (6)
PMCID: 5192452
PMID: 27983674
DOI: 10.3390/metabo6040046

[…] packages such as logic for structure elucidation (lsd) which is used to determine all possible molecular structures of an organic compound that are compatible with its spectroscopic data [,] and automics, a nmr metabolomics nmr alignment with integrated statistics []. additionally, there are a number of open-source databases such as the madison metabolomics consortium database (mmcd), […]

PMCID: 5037748
PMID: 27598144
DOI: 10.3390/ijms17091470

[…] and allantoate (δ1h = 5.23749, δ13c = 62.8906) signals., 1h nmr spectra. phased and baseline-corrected 1h nmr spectra were binned from 10.0 to 0.5 ppm with a bin width of 0.02 ppm using the software automics []. binning was performed applying the total scaling function of automics and the region from 5.0 to 4.6 ppm (hdo signal) was not binned. the matrix with the data of all the binned spectra […]

PMCID: 4876396
PMID: 27212081
DOI: 10.1038/srep26515

[…] d baseline corrected and calibrated using the internal standard (dss-d6)., phased and baseline-corrected 1h nmr spectra were binned from 8.0 to 0.5 ppm with a bin width of 0.02 ppm using the software automics. binning was performed applying the total scaling function of automics and the region from 5.0 to 4.6 ppm (hdo signal) was not binned. the matrix with the data of all the binned spectra (355  […]

PMCID: 4552000
PMID: 26315217
DOI: 10.1038/srep13548

[…] briefly, 1h-nmr data were reduced by subdividing the spectra into sequential 0.04 ppm designated regions between 1h chemical shifts of 0–9.5 ppm, and water resonance was excluded using automics (beta version 0.99 .1220). each region was integrated and normalized to the total of all resonance integral regions. the pca was run on r software using the scatterplot3d package. […]

PMCID: 4648061
PMID: 26329486
DOI: 10.1186/1475-925X-14-S2-S5

[…] precession signal, that is a crucial part of mr phenomenon, contains distortions that must be filtered out before signal analysis. one of such distortions is phase error., five popular algorithms: automics, shanon's entropy minimization, ernst's method, dispa and edispa are presented and discussed. a novel adaptive tuning algorithm for automics method was developed and numerically optimal […]


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Automics institution(s)
Beijing NMR Center, Peking University, Beijing, China; College of Life Sciences, Peking University, Beijing, China; College of Chemistry and Molecular Engineer, Peking University, Beijing, China; Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, China; No. 304 Hospital, Beijing, China; Chinese PLA General Hospital, Beijing, China
Automics funding source(s)
Supported by Grant 2009CB521703 from 973 Program of China and Grant 30125009 from NSFC.

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