Core 2: Software Infrastructure for Network Models and Cell Maps

核心 2：网络模型和小区地图的软件基础设施

• 批准号: 10525593
• 负责人: Trey Ideker
• 金额: $ 7.9万
• 依托单位: UNIVERSITY OF CALIFORNIA, SAN FRANCISCO
• 依托单位国家: 美国
• 财政年份: 2022
• 资助国家: 美国
• 起止时间: 2022-09-14 至 2027-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10525593
• 关键词: Back; Biological; Cell model; Cells; Code; Computer software; Custom; Data; Data Analyses; Deposition; Development; Docking; Ecosystem; Elements; Ensure; Environment; Generations; Genetic; Infrastructure; Lead; Libraries; Link; Maps; Ontology; Pathway Analysis; Proteomics; Publications; Publishing; Pythons; Research; Research Personnel; Resources; Scientist; Services; Software Framework; Software Tools; Visualization; Work; cancer cell; data dissemination; data exchange; data resource; digital object identifier; infrastructure development; network models; protein protein interaction; protein structure; public repository; repository; software infrastructure; tool; web app; web interface; web portal; web services; web site

CCMI v2.0 Core 2: Software Infrastructure for Network Models and Cell Maps Core Lead: Trey Ideker; Co-Investigator: Dexter Pratt SUMMARY The Software Infrastructure for Network Models and Cell Maps Core will support the CCMI Projects at all stages of research and publication. The core will provide infrastructure and assistance towards three main elements: (1) the Cytoscape desktop application along with tools and services from the Cytoscape Ecosystem; (2) NDEx, the Network Data Exchange; and (3) infrastructure for the development and deployment of web services and applications. First, we will support center investigators in use of the Cytoscape Ecosystem for analysis and visualization of biological networks, including protein--protein interaction networks from Project 1, genetic interaction networks from Project 2, and multiscale cancer cell maps from Project 3. The Cytoscape Ecosystem includes the well-known Cytoscape desktop environment, the HiView multiscale cell model viewer, the IQuery pathway analysis tool, multiple R and Python libraries, and the CDAPS software framework for the generation of multiscale cell models. Second, we will facilitate the use of NDEx by center investigators to publish CCMI cell maps, interaction data, and other products as “live” network data that can be immediately visualized and used. We will also provide assistance in the use of NDEx to share pre-publication network data between center investigators, including direct, programmatic access from Jupyter notebooks and other software. Third, we will provide assistance to Project 3 investigators in the creation of web interfaces and back-end services. For all projects, we will facilitate programmatic access to resources, hosting of websites, the use of Docker software containers, and the management of CCMI Github repositories. Finally, we will maintain and extend the CCMI web portal to provide access to (1) CCMI public networks and cell maps via the NDEx networks cloud, (2) CCMI software tools and resources, (3) custom websites and web applications CCMI v2.0

CCMI v2.0 核心 2：网络模型和小区地图的软件基础设施 核心负责人：Trey Ideker；联合研究员：Dexter Pratt 概括 网络模型和小区映射核心的软件基础设施将完全支持 CCMI 项目 核心将为三个主要阶段提供基础设施和援助。 要素：(1) Cytoscape 桌面应用程序以及来自 Cytoscape 生态系统的工具和服务； (2) NDEx，网络数据交换；以及 (3) 用于开发和部署网络的基础设施 首先，我们将支持中心研究人员使用 Cytoscape 生态系统进行研究。 生物网络的分析和可视化，包括项目 1 中的蛋白质-蛋白质相互作用网络， 来自项目 2 的遗传相互作用网络和来自项目 3 的多尺度癌细胞图谱。Cytoscape 生态系统包括著名的 Cytoscape 桌面环境、HiView 多尺度细胞模型查看器、 IQuery 通路分析工具、多个 R 和 Python 库以及 CDAPS 软件框架 其次，我们将促进中心研究人员使用 NDEx 进行发布。 CCMI 单元图、交互数据和其他产品作为“实时”网络数据，可以立即可视化 我们还将在使用 NDEx 之间共享预发布网络数据方面提供帮助。 中心调查人员，包括从 Jupyter 笔记本和其他软件直接进行编程访问。 我们将为项目 3 的研究人员提供创建 Web 界面和后端服务的帮助。 对于所有项目，我们将促进以编程方式访问资源、托管网站、使用 Docker 软件容器，以及 CCMI Github 存储库的管理最后，我们将维护和扩展。 CCMI 门户网站可通过 NDEx 网络云访问 (1) CCMI 公共网络和小区地图，(2) CCMI 软件工具和资源，(3) 自定义网站和 Web 应用程序 CCMI v2.0