CORE 1: Data Management and Bioinformatics

核心1：数据管理和生物信息学核心 总结 数据管理和生物信息学核心将在研究的各个阶段支持两个HPMI项目 和出版。核心将由三个主要部分组成：Cytoscape和Cytoscape 网络基础设施（CI）;网络数据交换（NDEx）;以及HPMI数据和分析门户。第一、 Cytoscape将为生物网络的分析和可视化提供一系列工具，包括 来自项目1的蛋白质-蛋白质相互作用网络，来自项目2的遗传相互作用网络，以及 两个项目的分层细胞本体和模型。第二个组件NDEx将提供 数据库基础设施，以支持网络数据和模型的共享、审查和传播。它将 还能够统一访问公共生物网络资源，供HPMI调查人员使用。最后， HPMI数据和分析门户将为软件工具和管道提供一个公共接入点， 相关数据。该组件将得到GenePattern Notebooks的支持，这将有助于 开发工作流程管道以及分析的共享和再现性。上述三 组件-Cytoscape中的可视化网络地图，NDEx中的网络和模型存储，以及软件和 GenePattern Notebooks中的分析工作流程-都将通过HPMI的网站访问。 使用HPMI产品的出版物将通过最近添加到Cytoscape中进行动态增强， 将网络数据嵌入同行评审期刊。最后，核心将利用一系列令人印象深刻的 超级计算的硬件基础设施，包括多个站点的高性能集群。

CORE 1: DATA MANAGEMENT AND BIOINFORMATICS CORE SUMMARY The ​Data Management and Bioinformatics Core will support the two HPMI projects at all stages of research and publication. The core will be composed of three major components: Cytoscape and the Cytoscape Cyberinfrastructure (CI); the Network Data Exchange (NDEx); and the HPMI Data and Analysis Portal. First, Cytoscape will provide a range of tools for the analysis and visualization of biological networks, including the protein-protein interaction networks from ​Project 1​, the genetic interaction networks from ​Project 2​, as well as the hierarchical cell ontologies and models from both projects. The second component, NDEx, will provide database infrastructure to support the sharing, review and dissemination of network data and models. It will also enable consolidated access to public biological network resources for use by HPMI investigators. Finally, the HPMI Data and Analysis Portal will provide a common access point for software tools and pipelines and for their associated data. This component will be supported by GenePattern Notebooks, which will facilitate the development of workflow pipelines and the sharing and reproducibility of analyses. The above three components – visual network maps in Cytoscape, storage of networks and models in NDEx, and software and analysis workflows in GenePattern​ Notebooks – will all be made accessible through the HPMI’s website. Publications using HPMI products will be enhanced by the recent additions to Cytoscape for dynamically embedding network data in peer-reviewed journals. Finally, the Core will draw on an impressive array of hardware infrastructure for supercomputing, including high performance clusters at multiple sites.