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

项目摘要 在过去的二十年里，癌症研究的前景随着公众对癌症的研究的激增而发生了变化。 现有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 复杂的计算方法和工具来整合和分析它们。把癌症研究 癌症研究界需要一种方法来轻松地将正确的工具和方法联合收割机结合起来， 分析和可视化与他们的研究相关的所有数据，并可重复地捕捉他们所拥有的历史 完了这些目标对于不编程的癌症生物学家来说可能特别令人生畏。基因模式 自2004年以来，计算基因组学环境一直为癌症研究人员服务，并通过以下方式得到增强： GenePattern Notebook，2017年发布。该提案的目标是继续支持、扩大和 增强基因模式生态系统。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，他们寻求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的和新兴的方法， 技术和不断变化的癌症研究环境。增加方法的范围， 方法提供给GenePattern社区，我们将提供无缝访问其他流行的'omic GenePattern Notebook中的分析包（Cytoscape、Galaxy、IGV），允许交叉使用方法 从同一个可执行笔记本中的多个包。我们还将提供查询支持， 访问托管在选定的癌症相关数据存储库上的数据。 目标2.继续为癌症研究社区撰写和提供GenePattern笔记本。我们将 为GenePattern-Notebook Workspace开发30-50个新的高实用性笔记本，利用Aim 1作为 这为用户提供了指导，一步一步地执行其综合分析。这些将包括 数据处理和分析工作流程，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实现托管， 高性能计算站点，并通过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推广、培训和支持。我们将致力于癌症研究 社区继续满足他们的需求。由癌症生物学家和医生组成的科学顾问委员会 科学家们将审查进展情况，并在我们继续进行的过程中指导我们的战略。我们将继续提供高度支持， 和推广GenePattern及其笔记本环境，包括以癌症为重点的教程和培训 材料、现场研讨会、会议演示、网络研讨会和社交媒体工具， 响应论坛我们将全面参与ITCR计划的所有活动。

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.