SGER GeneBeans: A Modular System That Makes Genomic-Scale Analysis Accessible to Biologists

生物学家现在可以访问大量的DNA序列和注释数据，但还没有工具集让新手很容易就这些大型序列数据集提出生物学问题。将创建一个具有可视化用户界面的环境，用于构建一系列查询和分析，而不需要用户看到基本的计算机代码。该系统将使用Enterprise JavaBeans(EJB)从各种来源导入序列数据，并将其存储在关系数据库中。其他EJB将处理工作流、查询数据库和分析结果。Ejb模块将被设计为将其结果提供给其他模块。该系统将是可扩展的，因为它将很容易添加采用适当接口的新模块。该系统将允许用户询问有关频率、相关性和重要性的问题，这些问题是数据挖掘方法的典型查询，而不需要编写新的程序。我们的系统原型将在历史悠久的黑人大学NCA&Amp；T的本科生课堂上进行测试，并用于植物DNA序列中的基因组结构研究。将设计新的搜索算法和统计分析，这些算法和统计分析很容易集成到我们的模块系统中，涉及到生物学研究生的跨学科培训。

Biologists now have access to vast amounts of DNA sequence and annotation data, but do not yet have tool sets that make it easy for a novice to ask biological questions about these large sequence data sets. An environment with a visual user interface for constructing series of queries and analyses without the need for the user to see the underlying computer code will be created. The system will use Enterprise JavaBeans (EJBs) to import sequence data from a variety of sources and store it in a relational database. Other EJBs will handle workflow, query the database, and analyze results. The EJB modules will be designed to make their results available to other modules. The system will be extensible in that it will be easy to add new modules that employ the appropriate interfaces. This system will allow users to ask questions about frequency, correlation, and significance, queries typical of data mining methods, without writing new programs. The prototype of our system will be tested both for undergraduate classroom use at a historically black university, NCA&T, and for research on genome structure in plant DNA sequences. New kinds of search algorithms and statistical analyses, which will be easily integrated into our modular system, will be designed involving the interdisciplinary training of a biology graduate student.