Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources
Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources
批准号:
10687189
负责人:
DAVID H HAUSSLER
金额:
$79.23万
依托单位国家:
美国
项目类别:
财政年份:
2021
资助国家:
美国
项目状态:
未结题
起止时间:
2021-09-01 至 2026-08-31
关键词:
AccelerationArchitectureAtlas of Cancer Mortality in the United StatesAuthorization documentationBiologyBrain NeoplasmsCellsChildChildhoodCollaborationsCommunitiesComplementComplexComputersDataData AnalysesData CollectionData CommonsData SetDatabasesDevelopmentDrug resistanceEducationEducational process of instructingEngineeringEnvironmentGalaxyGenomeGenomicsGenotype-Tissue Expression ProjectGrowthHumanHuman BioMolecular Atlas ProgramHuman GenomeIndividualIngestionInternationalInternetJointsLinkMalignant Childhood NeoplasmMapsMedicineMethodologyModelingMultiomic DataOrganoidsPediatric NeoplasmPerformancePopulationPre-Clinical ModelPrivatizationPublicationsResearchResearch PersonnelResourcesSamplingSecureStandardizationTissuesTrainingUpdateVisualizationVisualization softwareWorkanalytical toolanticancer researchcancer genomicscancer stem cellcloud baseddata accessdata harmonizationdata integrationdata resourcedata science infrastructuredata visualizationdesigndrug developmentgenome browsergenome resourcegenomic signatureimprovedindexinginsightlarge datasetsmultiple omicsnext generationnovel therapeuticsoutreachpatient derived xenograft modelpre-clinicalprototyperoutine practicescale uptherapeutic evaluationtooltranscriptome sequencingtumoruser centered designvirtual
中文摘要
摘要
癌症基因组学正在进行两个重要的范式转变:单细胞基因组分析和生长
NCI癌症研究数据共享区。单细胞基因组学正在改变我们对
复杂的肿瘤群体,揭示肿瘤组成,微环境,癌症干细胞
细胞和耐药性。几个大规模的,单细胞为重点的,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将影响几乎
生物学和医学的各个方面。为了使这些项目充分发挥其潜力,
必须有
使这些资源可访问的数据可视化和分析工具
一个广泛的生物医学组织,
研究人员然而,这是具有挑战性的,因为现有的数据可视化和分析工具根本无法扩展
来处理这些大型数据集。第二个范式转变是NCI开发的癌症研究数据
Commons(CRDC)是一个虚拟数据科学基础设施,将癌症研究数据收集与
分析工具,利用云的动态计算能力。高效、安全地纳入
广泛使用的第三方工具和平台,包括交互式可视化工具,如UCSC Xena,
需要CRDC使这一资源真正有用。随着这两种转变在世界范围内继续加速,
未来几年,它们将带来挑战和机遇。我们建议加强UCSC Xena,以支持和
通过四个目标实现这些转变。目标1.我们将把UCSC Xena扩展100倍,以支持
具有超过100万个细胞(更一般地,100万个生物实体)的数据集的可视化没有任何损失
数据或网络浏览器中的交互性。我们将利用计算机工程的一些新进展,
实现这一性能提升。此外,我们将开发三种新的可视化,使研究人员能够
更好地探索单细胞数据。目标2.我们将安全地将UCSC Xena与NCI CRDC中的资源集成
及其数据分析工具和平台社区。我们的集成将使加载结束分析
将结果转换为CRDC中的私有Xena Hub,以便在大型公共数据的背景下进行可视化,这是一种常规做法。
目标3:我们将通过扩展提供最新癌症基因组学资源数据的可视化
更新UCSC Xena数据库中的关键项目和数据集。我们将与树屋合作
儿童癌症倡议建立一个协调的临床前儿科基因组学数据资源,
在Xena浏览器上公开提供。这项工作将利用PDX模型和脑肿瘤类器官
豪斯勒博士的团队正在开发和分析目标4。我们将改进用户工作流程,
通过以用户为中心的设计参与,以及继续用户教育,支持和推广。
英文摘要
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.
期刊论文(2)
专著(0)
科研奖励(0)
会议论文
DOI:
10.48550/arxiv.2306.03255
发表时间:
2023-06
期刊:
ArXiv
影响因子:
--
作者:
[Awan Afiaz;Andrey Ivanov;J. Chamberlin;D. Hanauer;Candace Savonen;M. Goldman;M. Morgan;Michael Reich;Alexander Getka;Aaron N. Holmes;Sarthak Pati;D. Knight;P. Boutros;S. Bakas;J. Caporaso;G. Fiol;H. Hochheiser;Brian Haas;P. Schloss;James A. Eddy;Jake Albrecht;A. Fedorov;L. Waldron;Ava M. Hoffman;R. Bradshaw;J. Leek;Carrie Wright Department of Biostatistics;U. Washington;Seattle;Wa;Biostatistics Program;Public Health Sciences Division;Fred Hutchinson Cancer Research Center;Departmentof Pharmacology;Chemical Biology;Emory University School of Medicine;Emory University;Atlanta;Ga;Department of Biomedical Informatics;U. Utah;Salt lake City;Ut;Department of MathematicalStatistical Sciences;University of Michigan Medical School;A. Arbor;Mi;University of California at Santa Cruz;Santa Cruz;Ca;Roswell Park Comprehensive Cancer Center;Buffalo;Ny;U. California;San Diego;La Jolla;U. Pennsylvania;Philadelphia;Pa;Jonsson Comprehensive Cancer Center;Los Angeles;I. Health;Department of Genetics;Department of Urology;Pathogen;M. Institute;Northern Arizona University;Flagstaff;Az;U. Pittsburgh;Pittsburgh;Methods Development Laboratory;Broad Institute;Cambridge;Ma;D. Microbiology;Immunology;U. Michigan;Sage Bionetworks;D. Radiology;Brigham;Women's Hospital;H. School;Boston;D. Epidemiology;Biostatistics;City Health;Health Policy;New York.]
通讯作者:
Awan Afiaz;Andrey Ivanov;J. Chamberlin;D. Hanauer;Candace Savonen;M. Goldman;M. Morgan;Michael Reich;Alexander Getka;Aaron N. Holmes;Sarthak Pati;D. Knight;P. Boutros;S. Bakas;J. Caporaso;G. Fiol;H. Hochheiser;Brian Haas;P. Schloss;James A. Eddy;Jake Albrecht;A. Fedorov;L. Waldron;Ava M. Hoffman;R. Bradshaw;J. Leek;Carrie Wright Department of Biostatistics;U. Washington;Seattle;Wa;Biostatistics Program;Public Health Sciences Division;Fred Hutchinson Cancer Research Center;Departmentof Pharmacology;Chemical Biology;Emory University School of Medicine;Emory University;Atlanta;Ga;Department of Biomedical Informatics;U. Utah;Salt lake City;Ut;Department of MathematicalStatistical Sciences;University of Michigan Medical School;A. Arbor;Mi;University of California at Santa Cruz;Santa Cruz;Ca;Roswell Park Comprehensive Cancer Center;Buffalo;Ny;U. California;San Diego;La Jolla;U. Pennsylvania;Philadelphia;Pa;Jonsson Comprehensive Cancer Center;Los Angeles;I. Health;Department of Genetics;Department of Urology;Pathogen;M. Institute;Northern Arizona University;Flagstaff;Az;U. Pittsburgh;Pittsburgh;Methods Development Laboratory;Broad Institute;Cambridge;Ma;D. Microbiology;Immunology;U. Michigan;Sage Bionetworks;D. Radiology;Brigham;Women's Hospital;H. School;Boston;D. Epidemiology;Biostatistics;City Health;Health Policy;New York.
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]
通讯作者:
Goldman,MaryJ
Data Resource and Administrative Coordination Center for the Scalable and Systematic Neurobiology of Psychiatric and Neurodevelopmental Disorder Risk Genes Consortium
-
批准号:10642251
-
项目类别:
-
资助金额:$150.0万
-
财政年份:2023
-
负责人:DAVID H HAUSSLER
-
依托单位:
Center for Live Cell Genomics
-
批准号:10307037
-
项目类别:
-
资助金额:$250.64万
-
财政年份:2021
-
负责人:DAVID H HAUSSLER
-
依托单位:
Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources
-
批准号:10187394
-
项目类别:
-
资助金额:$76.69万
-
财政年份:2021
-
负责人:DAVID H HAUSSLER
-
依托单位:
Enhance UCSC Xena: extend interactive visualization to ultra-large-scale multi-omics data and integrate with analysis resources
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批准号:10430132
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项目类别:
-
资助金额:$75.16万
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财政年份:2021
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负责人:DAVID H HAUSSLER
-
依托单位:
Center for Live Cell Genomics
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批准号:10676332
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项目类别:
-
资助金额:$207.38万
-
财政年份:2021
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负责人:DAVID H HAUSSLER
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依托单位:
Nanoparticle Tracking Analyzer (NTA) for the Center for Live Cell Genomics
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批准号:10817569
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项目类别:
-
资助金额:$20.14万
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财政年份:2021
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负责人:DAVID H HAUSSLER
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依托单位:
Enabling Comparative Pangenomics
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批准号:10555318
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项目类别:
-
资助金额:$64.77万
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财政年份:2020
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负责人:DAVID H HAUSSLER
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依托单位:
Development of Advanced Preclinical Models for Pediatric Solid Tumors
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批准号:10579262
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项目类别:
-
资助金额:$58.95万
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财政年份:2020
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负责人:DAVID H HAUSSLER
-
依托单位:
Development of Advanced Preclinical Models for Pediatric Solid Tumors
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批准号:10356873
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项目类别:
-
资助金额:$58.95万
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财政年份:2020
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负责人:DAVID H HAUSSLER
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依托单位:
Center for Big Data in Translational Genomics
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批准号:9277519
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项目类别:
-
资助金额:$289.72万
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财政年份:2014
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负责人:DAVID H HAUSSLER
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依托单位:
Center for Big Data in Translational Genomics
-
批准号:9404121
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项目类别:
-
资助金额:$57.48万
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财政年份:2014
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负责人:DAVID H HAUSSLER
-
依托单位:
Center for Big Data in Translational Genomics
-
批准号:8935872
-
项目类别:
-
资助金额:$275.39万
-
财政年份:2014
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负责人:DAVID H HAUSSLER
-
依托单位:
Center for Big Data in Translational Genomics
-
批准号:9064923
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项目类别:
-
资助金额:$24.42万
-
财政年份:2014
-
负责人:DAVID H HAUSSLER
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依托单位:
Center for Big Data in Translational Genomics
-
批准号:9270741
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项目类别:
-
资助金额:$21.34万
-
财政年份:2014
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负责人:DAVID H HAUSSLER
-
依托单位:
Center for Big Data in Translational Genomics
-
批准号:8775080
-
项目类别:
-
资助金额:$199.67万
-
财政年份:2014
-
负责人:DAVID H HAUSSLER
-
依托单位:
Center for Big Data in Translational Genomics
-
批准号:9064924
-
项目类别:
-
资助金额:$44.13万
-
财政年份:2014
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负责人:DAVID H HAUSSLER
-
依托单位:
Center for Big Data in Translational Genomics
-
批准号:9270743
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项目类别:
-
资助金额:$46.03万
-
财政年份:2014
-
负责人:DAVID H HAUSSLER
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依托单位:
Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Canc
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批准号:8607380
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项目类别:
-
资助金额:$62.12万
-
财政年份:2013
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负责人:DAVID H HAUSSLER
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依托单位:
Cloud Based Resource for Data Hosting, Visualization and Analysis Using UCSC Canc
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批准号:8735909
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项目类别:
-
资助金额:$67.44万
-
财政年份:2013
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负责人:DAVID H HAUSSLER
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依托单位:
UCSC Center for Genomic Science and Minority Outreach Program
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批准号:7921323
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项目类别:
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资助金额:$69.0万
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财政年份:2009
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负责人:DAVID H HAUSSLER
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依托单位:
海外基金