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

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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.