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BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry.

Cao Y, Wang N, Ying X, Li A, Wang H, Zhang X, Li W - BMC Med Inform Decis Mak (2009)

Bottom Line: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis.By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, PR China. labs.net@gmail.com

ABSTRACT

Background: With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.

Results: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.

Conclusion: BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/.

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The main components of the BioSunMS. Four components are provided in BioSunMS system, which are Security and User Management, Data Management, MS data Processing, and MS profile Analysis, respectively.
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Figure 1: The main components of the BioSunMS. Four components are provided in BioSunMS system, which are Security and User Management, Data Management, MS data Processing, and MS profile Analysis, respectively.

Mentions: BioSunMS system includes four functional modules, namely, data management, spectrum processing, MS profile analysis and security module (Figure 1). The data management module provides a robust, client-server, relational database system for the management of patients information and MS data. Data are primarily stored in a relational database MySQL, while some raw data is stored on the file system (mainly to provide backup for MS data). The spectrum processing module performs spectrum import, spectrum export, and related analysis such as calibration, normalization and peak detection [20]. The MS profile module is designed for sample classification and identification of potential biomarkers. Background computations are mostly done by R package and libSVM [21]. BioSunMS has a security system for protecting the data. Access to any data can be controlled. Access is granted via user groups rather than individual users. The main features of BioSunMS can be found in Table 1.


BioSunMS: a plug-in-based software for the management of patients information and the analysis of peptide profiles from mass spectrometry.

Cao Y, Wang N, Ying X, Li A, Wang H, Zhang X, Li W - BMC Med Inform Decis Mak (2009)

The main components of the BioSunMS. Four components are provided in BioSunMS system, which are Security and User Management, Data Management, MS data Processing, and MS profile Analysis, respectively.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC2654546&req=5

Figure 1: The main components of the BioSunMS. Four components are provided in BioSunMS system, which are Security and User Management, Data Management, MS data Processing, and MS profile Analysis, respectively.
Mentions: BioSunMS system includes four functional modules, namely, data management, spectrum processing, MS profile analysis and security module (Figure 1). The data management module provides a robust, client-server, relational database system for the management of patients information and MS data. Data are primarily stored in a relational database MySQL, while some raw data is stored on the file system (mainly to provide backup for MS data). The spectrum processing module performs spectrum import, spectrum export, and related analysis such as calibration, normalization and peak detection [20]. The MS profile module is designed for sample classification and identification of potential biomarkers. Background computations are mostly done by R package and libSVM [21]. BioSunMS has a security system for protecting the data. Access to any data can be controlled. Access is granted via user groups rather than individual users. The main features of BioSunMS can be found in Table 1.

Bottom Line: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis.By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data.

View Article: PubMed Central - HTML - PubMed

Affiliation: Center of Computational Biology, Beijing Institute of Basic Medical Sciences, Taiping Road 27, Haidian district, Beijing 100850, PR China. labs.net@gmail.com

ABSTRACT

Background: With wide applications of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) and surface-enhanced laser desorption/ionization time-of-flight mass spectrometry (SELDI-TOF MS), statistical comparison of serum peptide profiles and management of patients information play an important role in clinical studies, such as early diagnosis, personalized medicine and biomarker discovery. However, current available software tools mainly focused on data analysis rather than providing a flexible platform for both the management of patients information and mass spectrometry (MS) data analysis.

Results: Here we presented a plug-in-based software, BioSunMS, for both the management of patients information and serum peptide profiles-based statistical analysis. By integrating all functions into a user-friendly desktop application, BioSunMS provided a comprehensive solution for clinical researchers without any knowledge in programming, as well as a plug-in architecture platform with the possibility for developers to add or modify functions without need to recompile the entire application.

Conclusion: BioSunMS provides a plug-in-based solution for managing, analyzing, and sharing high volumes of MALDI-TOF or SELDI-TOF MS data. The software is freely distributed under GNU General Public License (GPL) and can be downloaded from http://sourceforge.net/projects/biosunms/.

Show MeSH