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This article is part of the supplement: Eighth International Conference on Bioinformatics (InCoB2009): Computational Biology

Open Access Proceedings

Development of a database system for mapping insertional mutations onto the mouse genome with large-scale experimental data

Wenwei Yang12, Ke Jin2, Xing Xie3, Dongsheng Li3, Jigang Yang4, Li Wang3, Ning Gu3, Yang Zhong25 and Ling V Sun12*

Author Affiliations

1 Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, PR China

2 School of Life Sciences, Fudan University, Shanghai 200433, PR China

3 School of Computer Science, Fudan University, Shanghai 200433, PR China

4 School of Information Technology, Jiangnan University, Wuxi, Jiangsu 214122, PR China

5 Shanghai Center for Bioinformation Technology, Shanghai 200235, PR China

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BMC Genomics 2009, 10(Suppl 3):S7  doi:10.1186/1471-2164-10-S3-S7

Published: 3 December 2009

Abstract

Background

Insertional mutagenesis is an effective method for functional genomic studies in various organisms. It can rapidly generate easily tractable mutations. A large-scale insertional mutagenesis with the piggyBac (PB) transposon is currently performed in mice at the Institute of Developmental Biology and Molecular Medicine (IDM), Fudan University in Shanghai, China. This project is carried out via collaborations among multiple groups overseeing interconnected experimental steps and generates a large volume of experimental data continuously. Therefore, the project calls for an efficient database system for recording, management, statistical analysis, and information exchange.

Results

This paper presents a database application called MP-PBmice (insertional mutation mapping system of PB Mutagenesis Information Center), which is developed to serve the on-going large-scale PB insertional mutagenesis project. A lightweight enterprise-level development framework Struts-Spring-Hibernate is used here to ensure constructive and flexible support to the application. The MP-PBmice database system has three major features: strict access-control, efficient workflow control, and good expandability. It supports the collaboration among different groups that enter data and exchange information on daily basis, and is capable of providing real time progress reports for the whole project. MP-PBmice can be easily adapted for other large-scale insertional mutation mapping projects and the source code of this software is freely available at http://www.idmshanghai.cn/PBmice webcite.

Conclusion

MP-PBmice is a web-based application for large-scale insertional mutation mapping onto the mouse genome, implemented with the widely used framework Struts-Spring-Hibernate. This system is already in use by the on-going genome-wide PB insertional mutation mapping project at IDM, Fudan University.