建立基于公开软件的校园生物信息学平台

Establishment of campus wide bioinformatics platform using freeware

目的 :探讨建立适合我国国情的校园生物信息学平台的策略和方法 .方法 :以Emboss分子序列分析组件、R数理统计分析组件、Bioconductor基因芯片分析组件、Phylip分子进化研究工具、PostgreSQL关系数据库管理系统和Bioperl脚本语言为基本组件 ,在Linux操作系统上 ,将其编译、连接成为一个有机的校园生物信息学平台 .结果 :初步建成的校园生物信息学平台 ,可作为基于校园网的完整的核酸及蛋白质序列分析工具、基因芯片数据分析工具、对基因组数据进行多角度挖掘的工具、提供良好的新算法、新模型开发环境 .开放的框架使平台具有良好的可扩展性及向后的兼容性 .新开发的生物信息学工具可迅速整合进该平台 .结论 :用公开软件建立的校园生物信息学平台具有成本低和性能完善、优异的特点 。

AIM: To explore strategies for a campus wide bioinformatics platform. METHODS: Bioinformatics platform was built using freeware: Emboss was used as the molecular sequence analysis component, R as the biostatistical component, Bioconductor as the microarray data analysis component, Phylip as the molecular evolution study component, PostgreSQL as the relational database management system component, and Bioperl as script language component. All these components were compiled and linked on a personal computer under Linux Operating System. RESULTS: The established bioinformatics platform provided campus wide services for nucleic acid and protein sequence analysis, microarray data analysis, genome data mining, and algorithm and model development. The open infrastructure of our platform was of good inner flexibility and expansibility. CONCLUSION: The establishment of campus bioinformatics platform with freeware has the characteristics of low cost and excellent serviceability for postgenomic researches.