GenePattern and GenePattern Notebook: Integrative 'Omic Analysis for Cancer Research

项目摘要 在过去的二十年里，癌症研究的格局随着公开研究的爆炸性增长而改变 可用的和研究人员从不断发展的技术平台生成的数据集，以及越来越多的 用于集成和分析它们的复杂计算方法和工具。推动癌症研究 议程向前推进，癌症研究界需要一种方式来轻松地结合正确的工具和方法来 分析并可视化与他们的研究相关的所有数据，并可重复地捕获他们所拥有的历史 搞定了。对于没有编程的癌症生物学家来说，这些目标可能特别令人望而生畏。《基因模式》 计算基因组学环境自2004年以来一直为癌症研究人员提供服务，并通过 GenePattern Notebook，2017年发布。这项提议的目标是继续支持、扩大和 加强GenePattern生态系统。通过这些努力，我们将继续支持一个多元化的社区 处于癌症研究前沿的用户，他们试图更好地了解疾病的潜在机制， 将改进的患者诊断和预后方法转化为临床，并确定新的药物靶点。 目标1.确保GenePattern生态系统继续跟上新出现的方法和 技术和不断变化的癌症研究环境。增加方法和方法的范围 对于GenePattern社区可用的方法，我们将提供对其他流行的 GenePattern Notebook中的分析包(Cytoscape、Galaxy、IGV)，允许方法交错 来自同一可执行笔记本中的多个包。我们还将提供对查询和 访问托管在选定的癌症相关数据存储库中的数据。 目标2.继续为癌症研究社区编写和提供GenePattern笔记本。我们会 为GenePattern-Notebook工作区开发30-50台新的高实用笔记本电脑，利用Aim 1作为 需要，为用户提供指导，逐步执行他们的综合分析。这些措施将包括 数据处理和分析工作流，包括弥合从发现到转换的差距的方法。 目标3.扩展、维护和支持GenePattern生态系统基础设施。我们将继续支持 并增强GenePattern生态系统，包括在多个云架构上启用托管和高 性能计算站点，并使用高价值功能增强笔记本用户界面。 目标4.为我们的用户社区提供外展、培训和支持。我们将从事癌症研究 社区继续满足他们的需求。癌症生物学家和内科医生组成的科学咨询委员会 科学家们将审查进展并指导我们的战略。我们将继续提供高水平的支持 以及对GenePattern及其笔记本环境的宣传，包括以癌症为重点的教程和培训 材料、面对面研讨会、会议演示、网络研讨会和社交媒体工具以及我们的 响应性论坛。我们将全面参与ITCR项目的所有活动。

Project Summary Over the past two decades, the landscape of cancer research has changed with the explosion of publicly available and investigator generated datasets from evolving technology platforms, and the growing number of sophisticated computational methods and tools to integrate and analyze them. To move the cancer research agenda forward, the cancer research community needs a way to easily combine the right tools and methods to analyze and visualize all the data relevant to their studies, and reproducibly capture the history of what they have done. These objectives may be especially daunting for cancer biologists who don’t program. The GenePattern computational genomics environment has served cancer investigators since 2004 and was enhanced by GenePattern Notebook, released in 2017. The goal of this proposal is to continue to support, expand, and enhance the GenePattern ecosystem. Through these efforts we will continue to support a diverse community of users at the forefront of cancer research who seek to better understand the underlying mechanisms of disease, translate improved methods for patient diagnosis and prognosis to the clinic, and identify new drug targets. Aim 1. Ensure the GenePattern ecosystem continues to keep pace with new and emerging methods and technologies and the changing cancer research environment. To increase the range of methods and approaches available to the GenePattern community, we will provide seamless access to other popular ‘omic analysis packages (Cytoscape, Galaxy, IGV) within GenePattern Notebook, allowing the interleaving of methods from multiple packages within the same executable notebook. We will also provide support for querying and accessing data hosted on selected cancer-relevant data repositories. Aim 2. Continue to author and serve GenePattern notebooks for the cancer research community. We will develop 30-50 new high utility notebooks for the GenePattern-Notebook Workspace, leveraging Aim 1 as required, that provide users with guided, step-by-step execution of their integrative analysis. These will comprise data processing and analysis workflows, including approaches that bridge the gap from discovery to translation. Aim 3. Extend, maintain, and support the GenePattern ecosystem infrastructure. We will continue to support and enhance the GenePattern ecosystem, including enabling hosting on multiple cloud architectures and high- performance compute sites, and enhancing the Notebook user interface with high-value features. Aim 4. Provide outreach, training, and support to our user community. We will engage the cancer research community to continue to address their needs. A Scientific Advisory Board of cancer biologists and physician scientists will review progress and guide our strategy as we proceed. We will continue our high level of support and outreach for GenePattern and its notebook environment, including cancer-focused tutorials and training materials, in-person workshops, conference presentations, webinars, and social media vehicles and our responsive forum. We will fully participate in all of the ITCR program activities.