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Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.

Wang T, Shao K, Chu Q, Ren Y, Mu Y, Qu L, He J, Jin C, Xia B - BMC Bioinformatics (2009)

Bottom Line: Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results.Using Automics, users can complete spectral processing and data analysis within one software package in most cases.Moreover, with its open source architecture, interested researchers can further develop and extend this software based on the existing infrastructure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing NMR Center, Peking University, PR China. super_wt@sina.com

ABSTRACT

Background: Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public.

Results: In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion), data reduction (PCA, LDA, ULDA), unsupervised clustering (K-Mean) and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM). Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile.

Conclusion: Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases. Moreover, with its open source architecture, interested researchers can further develop and extend this software based on the existing infrastructure.

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Related in: MedlinePlus

Overlay display of 1D 1H NMR spectra automatically processed by Automics. The spectra were processed by automatic modules in the following steps: fast Fourier transform, phase correction (new introduced phase correction method), baseline correction (linear fitting) and peak alignment (global shift method).
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Figure 4: Overlay display of 1D 1H NMR spectra automatically processed by Automics. The spectra were processed by automatic modules in the following steps: fast Fourier transform, phase correction (new introduced phase correction method), baseline correction (linear fitting) and peak alignment (global shift method).

Mentions: Automics provides an efficient way for processing a large number of NMR spectra in batch mode by a series of automatic methods, and produces reasonably well corrected spectra. Figure 4 shows an example for displaying multiple processed spectra in Automics. For metabonomics studies, spectral processing results may have a significant impact on data analysis. The automatic spectral processing in Automics has the advantage that all NMR spectra are processed under the same criteria. This will potentially reduce systematic error due to the inconsistency of manual operations.


Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis.

Wang T, Shao K, Chu Q, Ren Y, Mu Y, Qu L, He J, Jin C, Xia B - BMC Bioinformatics (2009)

Overlay display of 1D 1H NMR spectra automatically processed by Automics. The spectra were processed by automatic modules in the following steps: fast Fourier transform, phase correction (new introduced phase correction method), baseline correction (linear fitting) and peak alignment (global shift method).
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2666662&req=5

Figure 4: Overlay display of 1D 1H NMR spectra automatically processed by Automics. The spectra were processed by automatic modules in the following steps: fast Fourier transform, phase correction (new introduced phase correction method), baseline correction (linear fitting) and peak alignment (global shift method).
Mentions: Automics provides an efficient way for processing a large number of NMR spectra in batch mode by a series of automatic methods, and produces reasonably well corrected spectra. Figure 4 shows an example for displaying multiple processed spectra in Automics. For metabonomics studies, spectral processing results may have a significant impact on data analysis. The automatic spectral processing in Automics has the advantage that all NMR spectra are processed under the same criteria. This will potentially reduce systematic error due to the inconsistency of manual operations.

Bottom Line: Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results.Using Automics, users can complete spectral processing and data analysis within one software package in most cases.Moreover, with its open source architecture, interested researchers can further develop and extend this software based on the existing infrastructure.

View Article: PubMed Central - HTML - PubMed

Affiliation: Beijing NMR Center, Peking University, PR China. super_wt@sina.com

ABSTRACT

Background: Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, researchers usually have to use multiple software packages for their studies because software packages generally focus on specific tasks. It would be beneficial to have a highly integrated platform, in which these tasks can be completed within one package. Moreover, with open source architecture, newly proposed algorithms or methods for spectral processing and data analysis can be implemented much more easily and accessed freely by the public.

Results: In this paper, we report an open source software tool, Automics, which is specifically designed for NMR-based metabonomics studies. Automics is a highly integrated platform that provides functions covering almost all the stages of NMR-based metabonomics studies. Automics provides high throughput automatic modules with most recently proposed algorithms and powerful manual modules for 1D NMR spectral processing. In addition to spectral processing functions, powerful features for data organization, data pre-processing, and data analysis have been implemented. Nine statistical methods can be applied to analyses including: feature selection (Fisher's criterion), data reduction (PCA, LDA, ULDA), unsupervised clustering (K-Mean) and supervised regression and classification (PLS/PLS-DA, KNN, SIMCA, SVM). Moreover, Automics has a user-friendly graphical interface for visualizing NMR spectra and data analysis results. The functional ability of Automics is demonstrated with an analysis of a type 2 diabetes metabolic profile.

Conclusion: Automics facilitates high throughput 1D NMR spectral processing and high dimensional data analysis for NMR-based metabonomics applications. Using Automics, users can complete spectral processing and data analysis within one software package in most cases. Moreover, with its open source architecture, interested researchers can further develop and extend this software based on the existing infrastructure.

Show MeSH
Related in: MedlinePlus