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


CONCLUSIONS
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.
Yang
Wenwei
W
Institute of Developmental Biology and Molecular Medicine, Fudan University, Shanghai 200433, PR China. wenwei_yang@fudan.edu.cn
Jin
Ke
K
Xie
Xing
X
Li
Dongsheng
D
Yang
Jigang
J
Wang
Li
L
Gu
Ning
N
Zhong
Yang
Y
Sun
Ling V
LV
D000818:Animals; D030561:Databases, Nucleic Acid; D016678:Genome; D020407:Internet; D051379:Mice; D016254:Mutagenesis, Insertional; D017422:Sequence Analysis, DNA / Q000379:methods*; D012985:Software Design