Department of Computer Science, Princeton University, Princeton, NJ 08540, USA.
BMC Bioinformatics. 2009 Dec 14;10:417. doi: 10.1186/1471-2105-10-417.
A wide variety of biological data can be modeled as network structures, including experimental results (e.g. protein-protein interactions), computational predictions (e.g. functional interaction networks), or curated structures (e.g. the Gene Ontology). While several tools exist for visualizing large graphs at a global level or small graphs in detail, previous systems have generally not allowed interactive analysis of dense networks containing thousands of vertices at a level of detail useful for biologists. Investigators often wish to explore specific portions of such networks from a detailed, gene-specific perspective, and balancing this requirement with the networks' large size, complex structure, and rich metadata is a substantial computational challenge.
Graphle is an online interface to large collections of arbitrary undirected, weighted graphs, each possibly containing tens of thousands of vertices (e.g. genes) and hundreds of millions of edges (e.g. interactions). These are stored on a centralized server and accessed efficiently through an interactive Java applet. The Graphle applet allows a user to examine specific portions of a graph, retrieving the relevant neighborhood around a set of query vertices (genes). This neighborhood can then be refined and modified interactively, and the results can be saved either as publication-quality images or as raw data for further analysis. The Graphle web site currently includes several hundred biological networks representing predicted functional relationships from three heterogeneous data integration systems: S. cerevisiae data from bioPIXIE, E. coli data using MEFIT, and H. sapiens data from HEFalMp.
Graphle serves as a search and visualization engine for biological networks, which can be managed locally (simplifying collaborative data sharing) and investigated remotely. The Graphle framework is freely downloadable and easily installed on new servers, allowing any lab to quickly set up a Graphle site from which their own biological network data can be shared online.
各种生物数据都可以建模为网络结构，包括实验结果（例如蛋白质-蛋白质相互作用）、计算预测（例如功能相互作用网络）或经过整理的结构（例如基因本体论）。虽然有几个工具可以用于全局水平上可视化大型图形或详细的小型图形，但以前的系统通常不允许对包含数千个顶点的密集网络进行交互式分析，而这些网络的详细程度对于生物学家来说是有用的。研究人员通常希望从详细的、特定基因的角度探索这些网络的特定部分，而平衡这种要求与网络的大规模、复杂结构和丰富的元数据是一个重大的计算挑战。
Graphle 是一个在线接口，用于访问任意无向、加权图形的大型集合，每个图形都可能包含数千个顶点（例如基因）和数亿个边（例如相互作用）。这些图形存储在一个集中的服务器上，并通过一个交互式 Java 小程序高效地访问。Graphle 小程序允许用户检查图形的特定部分，检索一组查询顶点（基因）周围的相关邻域。然后可以对该邻域进行交互式细化和修改，并将结果保存为出版质量的图像或原始数据，以进行进一步分析。Graphle 网站目前包括数百个生物网络，代表了来自三个异构数据集成系统的预测功能关系：来自 bioPIXIE 的 S. cerevisiae 数据、使用 MEFIT 的 E. coli 数据和来自 HEFalMp 的 H. sapiens 数据。
Graphle 是生物网络的搜索和可视化引擎，可以在本地进行管理（简化协作数据共享）和远程调查。Graphle 框架是免费下载的，并且易于在新服务器上安装，允许任何实验室都可以快速设置一个 Graphle 站点，从该站点可以在线共享他们自己的生物网络数据。
