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Open Access Highly Accessed Software

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

Tao Wang12, Kang Shao4, Qinying Chu5, Yanfei Ren2, Yiming Mu6, Lijia Qu2, Jie He4, Changwen Jin123 and Bin Xia123*

Author Affiliations

1 Beijing NMR Center, Peking University, Beijing, PR China

2 College of Life Sciences, Peking University, Beijing, PR China

3 College of Chemistry and Molecular Engineer, Peking University, Beijing, PR China

4 Cancer Institute & Hospital, Chinese Academy of Medical Sciences, Beijing, PR China

5 No. 304 Hospital, Beijing, PR China

6 Chinese PLA General Hospital, Beijing, PR China

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BMC Bioinformatics 2009, 10:83  doi:10.1186/1471-2105-10-83

Published: 16 March 2009

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.