National Center: Multiscale Analysis of Genomic and Cellular Networks (MAGNet)

国家中心：基因组和细胞网络的多尺度分析 (MAGNet)

• 批准号: 8012947
• 负责人: ANDREA CALIFANO
• 金额: $ 375.72万
• 依托单位: COLUMBIA UNIVERSITY HEALTH SCIENCES
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-09-26 至 2015-07-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/8012947
• 关键词: National; Center; Multiscale; Analysis; Genomic

A network of molecular interactions, involving many thousands of genes, their products, and other molecules, underlie cellular processes. Investigation of these interactions across a wide range of scales ranging from the formation/activation of transcriptional complexes, to the availability of a signaling pathway, all the way to macroscopic processes, such as cell adhesion, calls for a new level of sophistication in the design of genome- wide computational approaches. A homogeneous environment for the comprehensive mapping and analysis of molecular cellular interactions in would be a powerful resource for the biomedical research community. We propose the creation of a National Center for the Multiscale Analysis of Genomic and Cellular Networks (MAGNet). The Center will provide an integrative computational framework to organize molecular interactions in the cell into manageable context-dependent components and will develop interoperable computational models and tools that can leverage such a map of cellular interactions to elucidate important biological processes. Center activities will involve a significant, multidisciplinary effort of biological and computational sciences. Specific areas of expertise include natural language parsing (NLP), machine learning (ML), software systems and engineering, databases, computational structural biology, reverse engineering of genetic networks, biomedical literature datamining, and biomedical ontologies, among others. The Center will 1) construct an evidence integration framework to collect and fuse a variety of diverse cellular interaction clues based on their statistical relevance 2) assemble a comprehensive set of physics- and knowledge-based methodologies to fill this framework 3) provide a set of methodologies and filters, anchored in formal domain ontologies, to associated specific interactions to an organism, tissue, molecular, and cellular context. All relevant tools will be made accessible to the biomedical research community through a common, extensible, and interoperable software platform, geWorkbench. We will reach out to train and encourage researchers to use and/or develop new modules for, geWorkbench. An important element of the software platform will be the development of specific components that can exploit the evidence integration techniques developed by Core 9001 investigators to combine molecular interaction clues from Core 9002 algorithms and databases. Development will be both driven and tested by the biomedical community to ensure the usefulness of the tools and the usability of the graphical user interfaces to address biomedical problems in completely novel ways, to dissect the web of cellular interactions responsible for cellular processes and functions.

分子相互作用网络涉及数千个基因、其产物和其他分子，是细胞过程的基础。从转录复合物的形成/激活到信号通路的可用性，一直到细胞粘附等宏观过程，对这些相互作用进行广泛的研究，需要将全基因组计算方法的设计达到新的复杂程度。用于全面绘制和分析分子细胞相互作用的同质环境将成为生物医学研究界的强大资源。我们建议建立国家基因组和细胞网络多尺度分析中心（MAGNet）。该中心将提供一个综合计算框架，将细胞中的分子相互作用组织成可管理的上下文相关组件，并将开发可互操作的计算模型和工具，可以利用这种细胞相互作用图来阐明重要的生物过程。中心活动将涉及生物和计算科学的重大、多学科努力。具体的专业领域包括自然语言解析（NLP）、机器学习（ML）、软件系统和工程、数据库、计算结构生物学、遗传网络逆向工程、生物医学文献数据挖掘和生物医学本体等。该中心将 1) 构建一个证据整合框架，根据其统计相关性收集和融合各种不同的细胞相互作用线索 2) 组装一套全面的基于物理和知识的方法来填充该框架 3) 提供一套锚定在正式领域本体中的方法和过滤器，以与有机体、组织、分子和细胞环境相关的特定相互作用。所有相关工具都将通过通用、可扩展和可互操作的软件平台 geWorkbench 向生物医学研究界提供。我们将提供培训并鼓励研究人员使用和/或开发 geWorkbench 的新模块。该软件平台的一个重要组成部分将是开发特定组件，这些组件可以利用 Core 9001 研究人员开发的证据集成技术，将来自 Core 9002 算法和数据库的分子相互作用线索结合起来。开发将由生物医学界推动和测试，以确保工具的有用性和图形用户界面的可用性，以全新的方式解决生物医学问题，剖析负责细胞过程和功能的细胞相互作用网络。