Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis
<p>Abstract</p> <p>Background</p> <p>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 u...
| Main Authors: | , , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
BMC
2009-03-01
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| Series: | BMC Bioinformatics |
| Online Access: | http://www.biomedcentral.com/1471-2105/10/83 |
| _version_ | 1828411547111653376 |
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| author | Qu Lijia Mu Yiming Ren Yanfei Chu Qinying Shao Kang Wang Tao He Jie Jin Changwen Xia Bin |
| author_facet | Qu Lijia Mu Yiming Ren Yanfei Chu Qinying Shao Kang Wang Tao He Jie Jin Changwen Xia Bin |
| author_sort | Qu Lijia |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p> |
| first_indexed | 2024-12-10T12:31:59Z |
| format | Article |
| id | doaj.art-4274e87845d74526ae52dff15369eada |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-10T12:31:59Z |
| publishDate | 2009-03-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-4274e87845d74526ae52dff15369eada2022-12-22T01:48:46ZengBMCBMC Bioinformatics1471-21052009-03-011018310.1186/1471-2105-10-83Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysisQu LijiaMu YimingRen YanfeiChu QinyingShao KangWang TaoHe JieJin ChangwenXia Bin<p>Abstract</p> <p>Background</p> <p>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.</p> <p>Results</p> <p>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.</p> <p>Conclusion</p> <p>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.</p>http://www.biomedcentral.com/1471-2105/10/83 |
| spellingShingle | Qu Lijia Mu Yiming Ren Yanfei Chu Qinying Shao Kang Wang Tao He Jie Jin Changwen Xia Bin Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis BMC Bioinformatics |
| title | Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis |
| title_full | Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis |
| title_fullStr | Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis |
| title_full_unstemmed | Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis |
| title_short | Automics: an integrated platform for NMR-based metabonomics spectral processing and data analysis |
| title_sort | automics an integrated platform for nmr based metabonomics spectral processing and data analysis |
| url | http://www.biomedcentral.com/1471-2105/10/83 |
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