Institute for Systems Biology, Seattle, WA 98103, USA.
Proteomics. 2011 Jan;11(1):154-8. doi: 10.1002/pmic.201000459. Epub 2010 Dec 6.
The Protein Information and Property Explorer 2 (PIPE2) is an enhanced software program and updated web application that aims at providing the proteomic researcher a simple, intuitive user interface through which to begin inquiry into the biological significance of a list of proteins typically produced by MS/MS proteomic processing software. PIPE2 includes an improved interface, new data visualization options, and new data analysis methods for combining disparate, but related, data sets. In particular, PIPE2 has been enhanced to handle multi-dimensional data such as protein abundance, gene expression, and/or interaction data. The current architecture of PIPE2, modeled after that of Gaggle (a programming infrastructure for interoperability between separately developed software tools), contains independent functional units that can be instantiated and pieced together at the user's discretion to form a pipelined analysis workflow. Among these functional units is the Network Viewer component, which adds rich network analysis capabilities to the suite of existing proteomic web resources. Additionally, PIPE2 implements a framework within which new analysis procedures can be easily deployed and distributed over the World Wide Web. PIPE2 is available as a web service at http://pipe2.systemsbiology.net/.
蛋白质信息和特性探索者 2 （PIPE2）是一个经过增强的软件程序和更新的网络应用程序，旨在为蛋白质组学研究人员提供一个简单、直观的用户界面，通过该界面可以开始查询一组由 MS/MS 蛋白质组学处理软件通常产生的蛋白质的生物学意义。PIPE2 包括一个改进的界面、新的数据可视化选项以及用于组合不同但相关数据集的新数据分析方法。特别是，PIPE2 已得到增强，可以处理多维数据，例如蛋白质丰度、基因表达和/或相互作用数据。PIPE2 的当前架构是在 Gaggle（用于独立开发的软件工具之间互操作的编程基础结构）的基础上建模的，包含独立的功能单元，这些功能单元可以根据用户的决定实例化并组合在一起，形成流水线分析工作流程。这些功能单元之一是网络查看器组件，它为现有的蛋白质组学网络资源套件添加了丰富的网络分析功能。此外，PIPE2 实现了一个框架，在该框架内可以轻松部署和分发新的分析程序，并且可以通过万维网访问。PIPE2 作为网络服务可在 http://pipe2.systemsbiology.net/ 上使用。
