NDEx - the Network Data Exchange A Network Commons for Biologists

总结 癌症标志网络的知识是解释分子异质性的关键 可见于肿瘤内部和肿瘤之间。NDEx，网络数据交换（www.ndexbio.org），是一个在线的 科学家可以上传，共享和公开分发分子网络和途径的公共空间 模型我们目前已经进入了国家癌症研究所（U24）为期三年的资助的第二年 CA 184427 A），在此期间，我们创建了NDEx开源平台; 一个公共网站;并开始将NDEx链接到Cytoscape等应用程序。在建立了这个最初的 系统，我们下一个资助期的目标是快速开发NDEx网络内容， 社区以及这些资源影响癌症研究和治疗的方式。在 特别是，我们将（1）将NDEx网络连接到下一代癌症基因组分析;（2） 实现期刊网站直接发布互动网络;（3）发展特色期刊 通过社会组织和自动化的癌症途径内容;和（4）扩展NDEx 框架，以支持不断增长的用户和分析工具社区。通过这些目标， NDEx项目的重点从核心基础设施过渡到基因组分析工作流程， 癌症相关的网络内容，出版和社区建设。这些事态发展涉及一个 癌症研究迫切需要一个能够分析基因组规模的网络基础设施 分子网络中的信息。

Summary Knowledge of the hallmark networks of cancer has been key to interpreting the molecular heterogeneity seen within and across tumors. NDEx, the Network Data Exchange (www.ndexbio.org), is an online commons where scientists can upload, share, and publicly distribute molecular networks and pathway models. We are currently two years into a three-year grant from the National Cancer Institute (U24 CA184427A), during which time we have created the NDEx open-source platform; released NDEx as a public website; and begun to link NDEx to applications such as Cytoscape. Having built this initial system, our goals for the next funding period are to rapidly develop NDEx network content and communities and the means by which these resources impact cancer research and treatment. In particular, we will (1) Connect NDEx networks to next-generation cancer genome analysis; (2) Enable the direct publishing of interactive networks on journal websites; (3) Develop hallmark cancer pathway content via social organization and automation; and (4) Scale the NDEx framework to support a growing community of users and analysis tools. Through these aims, the emphasis of the NDEx Project transitions from core infrastructure to genome analysis workflows, cancer-relevant network content, publishing, and community building. These developments address a strong and immediate need in cancer research for a cyberinfrastructure that can analyze genome-scale information in the context of molecular networks.