MAGMA: analysis of two-channel microarrays made easy.
MAGMA: analysis of two-channel microarrays made easy.
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DOI：
10.1093/nar/gkm302
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发表时间：
2007-07
影响因子：
14.9
通讯作者：
Schlapbach R
中科院分区：
文献类型：
--
作者：
Rehrauer H;Zoller S;Schlapbach R
网络应用程序MAGMA提供了一个简单直观的界面，以确定差异表达的基因从双通道微阵列数据。虽然底层算法并不上级于类似的Web应用程序，但MAGMA特别用户友好，无需事先培训即可使用。用户界面引导新手用户完成最典型的微阵列分析工作流程，包括数据上传、注释、标准化和统计分析。它自动生成R脚本，记录MAGMA的整个数据处理步骤，从而允许用户在本地R安装中重新生成所有结果。MAGMA的实现遵循模型-视图-控制器的设计模式，严格分离基于R的统计数据处理，Web表示和应用程序逻辑。这种模块化设计使得应用程序灵活，易于扩展的领域之一的专家：统计微阵列分析，网页设计或软件开发。最先进的Java Server Faces技术用于生成Web界面和执行用户输入处理。MAGMA的面向对象的模块化框架使其易于扩展和适用于其他领域，并表明现代Java技术也适用于相当小而简洁的学术项目。MAGMA可在www.magag-fgcz.uzh.ch上免费查阅。
The web application MAGMA provides a simple and intuitive interface to identify differentially expressed genes from two-channel microarray data. While the underlying algorithms are not superior to those of similar web applications, MAGMA is particularly user friendly and can be used without prior training. The user interface guides the novice user through the most typical microarray analysis workflow consisting of data upload, annotation, normalization and statistical analysis. It automatically generates R-scripts that document MAGMA's entire data processing steps, thereby allowing the user to regenerate all results in his local R installation. The implementation of MAGMA follows the model-view-controller design pattern that strictly separates the R-based statistical data processing, the web-representation and the application logic. This modular design makes the application flexible and easily extendible by experts in one of the fields: statistical microarray analysis, web design or software development. State-of-the-art Java Server Faces technology was used to generate the web interface and to perform user input processing. MAGMA's object-oriented modular framework makes it easily extendible and applicable to other fields and demonstrates that modern Java technology is also suitable for rather small and concise academic projects. MAGMA is freely available at www.magma-fgcz.uzh.ch.