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Automics specifications


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


No version available


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

Publication for Automics

Automics citations


Recommended strategies for spectral processing and post processing of 1D 1H NMR data of biofluids with a particular focus on urine

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

[…] ompound 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 (CS […]


Current and Future Perspectives on the Structural Identification of Small Molecules in Biological Systems

PMCID: 5192452
PMID: 27983674
DOI: 10.3390/metabo6040046

[…] ated 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), consist […]


Cannibalism Affects Core Metabolic Processes in Helicoverpa armigera Larvae—A 2D NMR Metabolomics Study

Int J Mol Sci
PMCID: 5037748
PMID: 27598144
DOI: 10.3390/ijms17091470

[…] 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 (4 […]


Artificial Autopolyploidization Modifies the Tricarboxylic Acid Cycle and GABA Shunt in Arabidopsis thaliana Col 0

Sci Rep
PMCID: 4876396
PMID: 27212081
DOI: 10.1038/srep26515
call_split See protocol

[…] 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  […]


Probiotic Bifidobacterium longum alters gut luminal metabolism through modification of the gut microbial community

Sci Rep
PMCID: 4552000
PMID: 26315217
DOI: 10.1038/srep13548

[…] modifications. 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. Each coordi […]


Strategies for optimizing the phase correction algorithms in Nuclear Magnetic Resonance spectroscopy

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

[…] in results obtained for with tuning was noticed. For all five algorithms the values of relative phase error are worse while compared to the low noise level results. The best results were obtained for Automics algorithm. It was also observed that addition of higher-level noise increases the dispersion of spectra generated for same combination of φ0 and φ1 values. With low noise this value was equal […]


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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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