Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources

增强 UCSC Xena：将交互式可视化扩展到超大规模多组学数据并与分析资源集成

• 批准号: 10687189
• 负责人: DAVID H HAUSSLER
• 金额: $ 79.23万
• 依托单位: UNIVERSITY OF CALIFORNIA SANTA CRUZ
• 依托单位国家: 美国
• 财政年份: 2021
• 资助国家: 美国
• 起止时间: 2021-09-01 至 2026-08-31
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10687189
• 关键词: Acceleration; Architecture; Atlas of Cancer Mortality in the United States; Authorization documentation; Biology; Brain Neoplasms; Cells; Child; Childhood; Collaborations; Communities; Complement; Complex; Computers; Data; Data Analyses; Data Collection; Data Commons; Data Set; Databases; Development; Drug resistance; Education; Educational process of instructing; Engineering; Environment; Galaxy; Genome; Genomics; Genotype-Tissue Expression Project; Growth; Human; Human BioMolecular Atlas Program; Human Genome; Individual; Ingestion; International; Internet; Joints; Link; Malignant Childhood Neoplasm; Maps; Medicine; Methodology; Modeling; Multiomic Data; Organoids; Pediatric Neoplasm; Performance; Population; Pre-Clinical Model; Privatization; Publications; Research; Research Personnel; Resources; Sampling; Secure; Standardization; Tissues; Training; Update; Visualization; Visualization software; Work; analytical tool; anticancer research; cancer genomics; cancer stem cell; cloud based; data access; data harmonization; data integration; data resource; data science infrastructure; data visualization; design; drug development; genome browser; genome resource; genomic signature; improved; indexing; insight; large datasets; multiple omics; next generation; novel therapeutics; outreach; patient derived xenograft model; pre-clinical; prototype; routine practice; scale up; therapeutic evaluation; tool; transcriptome sequencing; tumor; user centered design; virtual

Abstract Two significant paradigm shifts are underway in cancer genomics: single-cell genomic profiling and the growth of the NCI Cancer Research Data Commons. Single-cell genomics is transforming our understanding of complex tumor populations and revealing new insights into tumor composition, microenvironment, cancer stem cells, and drug resistance. Several large-scale, single-cell-focused, national and international projects are currently underway, including HCA, HTAN, and HuBMAP. Data generated by these projects will impact almost every aspect of biology and medicine. For these projects to realize their full potential, it is essential to have data visualization and analysis tools that make these resources accessible to a broad group of biomedical researchers. This is challenging, however, as existing data visualization and analysis tools simply cannot scale to handle these large datasets. The second paradigm shift is NCI’s development of the Cancer Research Data Commons (CRDC), a virtual data science infrastructure that connects cancer research data collections with analytical tools, leveraging the dynamic computing power of the cloud. Efficient and secure incorporation of widely-used 3rd party tools and platforms, including interactive visualization tools such as UCSC Xena, into CRDC is needed to make this resource truly useful. As both of these transitions continue to accelerate in the coming years, they present challenges and opportunities. We propose to enhance UCSC Xena to support and enable these transitions through four aims. Aim 1. We will scale up UCSC Xena by 100x to support the visualization of datasets with greater than 1 million cells (more generally, 1 million bio-entities) without any loss of data or interactivity in the web browser. We will employ several new advances in computer engineering to achieve this performance gain. In addition, we will develop three new visualizations to enable researchers to better explore single-cell data. Aim 2. We will securely integrate UCSC Xena with resources in the NCI CRDC and its community of data analysis tools and platforms. Our integration will make loading ending analysis results into a private Xena Hub in CRDC for visualization in the context of large public data a routine practice. Aim 3. We will provide visualization of the most current cancer genomics resource data through the expansion and update of UCSC Xena database with key projects and datasets. We will collaborate with the Treehouse Childhood Cancer Initiative to build a harmonized preclinical pediatric genomics data resource and make it publicly available on the Xena Browser. This work will leverage PDX models and brain tumor organoids currently being developed and profiled by Dr. Haussler’s group. Aim 4. We will improve user workflows and engagement through User Centered Design, as well as continue user education, support, and outreach.

抽象的 癌症基因组学的两个显着范式转移正在进行中：单细胞基因组分析和生长 NCI癌症研究数据共享。单细胞基因组学正在改变我们对 复杂的肿瘤种群，并揭示了对肿瘤组成，微环境，癌症的新见解 细胞和耐药性。几个大规模的，专注于单细胞的国家和国际项目是 目前正在进行中，包括HCA，HTAN和HUBMAP。这些项目产生的数据几乎会影响 生物学和医学的各个方面。为了使这些项目发挥其全部潜力， 必须拥有 数据可视化和分析工具，使这些资源可访问 到一群生物医学 研究人员。但是，这是挑战，因为现有的数据可视化和分析工具根本无法扩展 处理这些大数据集。第二个范式转移是NCI的癌症研究数据的发展 Commons（CRDC），一种虚拟数据科学基础设施，将癌症研究数据收集联系起来 分析工具，利用云的动态计算能力。高效且安全的就业 广泛使用的第三方工具和平台，包括UCSC Xena等交互式可视化工具， 需要CRDC才能使此资源真正有用。随着这两个转变在 未来几年，他们提出了挑战和机遇。我们建议增强UCSC Xena以支持和 通过四个目标启用这些过渡。目标1。我们将通过100倍扩大UCSC Xena，以支持 具有超过100万个单元（更一般的100万个生物本性）的数据集的可视化数据集，而不会损失任何损失 网络浏览器中的数据或交互性。我们将在计算机工程方面采用一些新的进步 实现这一绩效增长。此外，我们将开发三个新的可视化，以使研究人员能够 更好地探索单细胞数据。 AIM 2。我们将安全地将UCSC Xena与NCI CRDC中的资源整合在一起 及其数据分析工具和平台社区。我们的集成将使加载端分析 在大型公共数据的情况下，在CRDC中的私人Xena中心进行可视化。 AIM 3。我们将通过扩展提供最新的癌症基因组学资源数据的可视化 并使用关键项目和数据集更新UCSC XENA数据库。我们将与树屋合作 儿童癌症倡议旨在建立统一的临床前基因组学数据资源并实现 在Xena浏览器上公开可用。这项工作将利用PDX型号和脑肿瘤器官 目前是由Haussler博士小组开发和介绍的。目标4。我们将改善用户工作流程和 通过以用户为中心的设计进行参与，并继续进行用户教育，支持和外展。

项目成果

Reviewers: intercept weaponization of genetics.

评论家：拦截遗传学武器化。

• DOI: 10.1038/d41586-023-00218-7
• 发表时间: 2023
• 期刊: Nature
• 影响因子: 64.8
• 作者: Goldman,MaryJ