最近项目要使用到可视化分析工具Cytoscape,所以会花费很多的时间跟精力来整理Cytoscape软件使用和开发的相关资料，希望写下的文章能减少有兴趣的同行学习跟开发所走的弯路时间、同时也是因为百度跟CodeProject的资料太少，所以只能靠官网文档来慢慢摸索，不当之处望指出，大家一起进步。

官网: http://www.cytoscape.org/

源码网址https://github.com/cytoscape/cytoscape-impl

下载源码并解压缩到D:\cytoscape-impl-develop

安装好JDK1.7版本的软件

安装好IntelliJ IDEA 13.1.4软件，系统自动提示升级到IntelliJ IDEA 13.1.5版本

使用IntelliJ IDEA 13.1.5打开刚解压缩的D:\cytoscape-impl-develop目录对应的项目

等待IntelliJ IDEA软件下载所需的jar包

相关介绍:

Cytoscape is an open source software platform for visualizing molecular interaction networks and biological pathways and integrating these networks with annotations, gene expression profiles and other state data. Although Cytoscape was originally designed for biological research, now it is a general platform for complex network analysis and visualization.   Cytoscape coredistribution provides a basic set of features for data integration, analysis, and visualization.   Additional features are available as Apps (formerly calledPlugins).   Apps are available for network and molecular profiling analyses, new layouts, additional file format support, scripting, and connection with databases.

     Cytoscape是一款开源可视化软件，其可用于整合模块化网络和生物科学联系网络图的绘制。虽然起初是为生物研究设计，但现在也可以用于复杂网络的分析和可视化呈现。其也可以通过插件扩展丰富自身的功能。

     Cytoscape的部分源码可以在https://github.com/cytoscape/cytoscape-impl 中下载到。------部分源码可得（GitHub上有源码）