Core 1

核心1

• 批准号: 9335910
• 负责人: ERIC A SOBIE
• 金额: $ 6.75万
• 依托单位: ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI
• 依托单位国家: 美国
• 财政年份: 2007
• 资助国家: 美国
• 起止时间: 2007-09-18 至 2019-08-31
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/9335910
• 关键词: Adverse drug effect; Communities; Data; Data Analyses; Databases; Development; Education and Outreach; Gene Proteins; Genes; Genomics; Goals; Heart; Imagery; Internet; Libraries; Modeling; New York; Online Systems; Pathway Analysis; Pharmaceutical Preparations; Phonation; Progress Reports; Property; Protein Kinase; Proteomics; Regulator Genes; Research; Running; Signal Transduction; Standardization; Substrate Interaction; Systems Biology; Tablets; Telephone; Visualization software; data visualization; experience; new technology; programs; protein protein interaction; simulation; three-dimensional modeling; tool; web interface

Approach 1. Network Analysis and Visualization: We will support the four research themes by developing data analysis tools and databases, as well as by participating in data analysis for projects with external collaborators. We will provide ongoing support for analysis of genomic and proteomic data. Initial analysis of the genomic and proteomic data to identify statistical differences caused by the various perturbations will be done within these facilities. Once the changes are identified, the differentially modulated gene/proteins will be used to develop networks, and classifiers in Theme 1 and the data from these analyses will be transferred to the Core for visualization and distribution to the research community. We will continue the development of web-based applications to support interactive visualization of networks and dynamical models. We have extensive experience in the development and distribution of such web based programs as have been described in the Progress Report Section (19, 21, 24, 26, 27, 29-32, 47, 50). In the coming term we will use newer technologies such as HTML5 including the implementation of the features offered by D3, a new JavaScript library for data visualization. We will maintain a mySQL database that contains information about drug properties, drug-drug networks, gene properties, gene regulatory networks, protein-protein interactions, protein kinase-substrate interactions, cell signaling networks and data from quantitative dynamical models. In addition, since HTML5 offers easy Mobile integration we will launch several of the web-based applications for Mobile use as phone and tablet Apps. As part of the research themes we plan to develop a web-interface for the drug/side-effect classifier proposed for Theme 1. We will develop web visualization for the both the underlying networks and the dynamical models that will be developed in Themes 2 and 3. This will enable the wide dissemination of these models so that they can be used by others. For Theme 4 we will develop the heart 3D models as an interactive online tool where users will be able to tune parameters and run simulations online.

方法1。网络分析和可视化：我们将通过开发数据分析工具和数据库以及与外部合作者的项目参与数据分析来支持四个研究主题。我们将为分析基因组和蛋白质组学数据提供持续的支持。对基因组和蛋白质组学数据的初步分析，以识别由各种扰动引起的统计差异。一旦确定了变化，差异调制的基因/蛋白质将用于开发网络，主题1中的分类器以及这些分析的数据将转移到可视化和分布到研究界的核心。 我们将继续开发基于Web的应用程序，以支持网络和动态模型的交互式可视化。我们在进度报告部分（19、21、24、26、27、29-32、47、50）中所述的基于Web的程序的开发和分发方面具有丰富的经验。在接下来的学期中，我们将使用诸如HTML5之类的较新技术，包括实现D3提供的功能，该功能是一个新的JavaScript库进行数据可视化。我们将维护一个MySQL数据库，该数据库包含有关药物特性，药物 - 药物网络，基因特性，基因调节网络，蛋白质 - 蛋白质相互作用，蛋白激酶 - 基底相互作用，细胞信号网络和来自定量动力学模型的数据的信息。此外，由于HTML5提供了简单的移动集成，因此我们将启动一些基于Web的应用程序，以作为手机和平板电脑应用程序。作为研究主题的一部分，我们计划为主题1提出的药物/副作用分类器开发一个网络接口。我们将为基础网络和将在主题2和3中开发的动态模型开发网络可视化。这将促进这些模型的广泛传播，以便它们可以被其他模型使用。对于主题4，我们将开发心脏3D模型作为交互式在线工具，用户将能够在线调整参数并在线运行模拟。