The UCSC Genome Browser

UCSC 基因组浏览器

基本信息

批准号：
10411053
负责人：
Maximilian Haeussler
金额：
$ 398.37万
依托单位：
UNIVERSITY OF CALIFORNIA SANTA CRUZ
依托单位国家：
美国
项目类别：
财政年份：
2001
资助国家：
美国
起止时间：
2001-07-12 至 2027-04-30
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/10411053
关键词：
Address Algorithms Alleles Animal Model Animals Archives Biochemical Biological Assay Cells Chromosomes Clinical Code Complex Computer Analysis Computer software Custom DNA DNA sequencing Data Data Reporting Data Set Data Sources Databases Designer Drugs Diploidy Disease Disease Progression Documentation Drug Design Ecosystem Engineering Ensure Ethnic Origin European Eye Gene Family Generations Genes Genetic Diseases Genetic Variation Genetic study Genome Genomics Haploidy Human Human Genome Individual Infrastructure Intelligence Internet Maps Medical Mitochondria Modernization Molecular Mus National Human Genome Research Institute Noise Patient Care Performance Personally Identifiable Information Persons Physiology Population Publications Publishing Reproducibility Research Research Personnel Resources Sampling Science Scientist Sequence Analysis Series Source System Technology Testing Text Tissues Transcript Underrepresented Minority Underserved Population Untranslated RNA Update Variant Visualization Visualization software Work annotation system base biomedical resource data access data integration design diverse data drug-sensitive experience gene function genetic variant genome annotation genome browser genomic data human pangenome improved member new technology outreach pan-genome programs protein protein interaction reference genome repository side effect single cell technology single molecule single-cell RNA sequencing software development therapy design tool web site web-based tool

Address Algorithms Alleles Animal Model Animals Archives Biochemical Biological Assay Cells Chromosomes Clinical Code Complex Computer Analysis Computer software Custom DNA DNA sequencing Data Data Reporting Data Set Data Sources Databases Designer Drugs Diploidy Disease Disease Progression Documentation Drug Design Ecosystem Engineering Ensure Ethnic Origin European Eye Gene Family Generations Genes Genetic Diseases Genetic Variation Genetic study Genome Genomics Haploidy Human Human Genome Individual Infrastructure Intelligence Internet Maps Medical Mitochondria Modernization Molecular Mus National Human Genome Research Institute Noise Patient Care Performance Personally Identifiable Information Persons Physiology Population Publications Publishing Reproducibility Research Research Personnel Resources Sampling Science Scientist Sequence Analysis Series Source System Technology Testing Text Tissues Transcript Underrepresented Minority Underserved Population Untranslated RNA Update Variant Visualization Visualization software Work annotation system base biomedical resource data access data integration design diverse data drug-sensitive experience gene function genetic variant genome annotation genome browser genomic data human pangenome improved member new technology outreach pan-genome programs protein protein interaction reference genome repository side effect single cell technology single molecule single-cell RNA sequencing software development therapy design tool web site web-based tool

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项目摘要

ABSTRACT The UCSC Genome Browser and associated tools are used by hundreds of thousands of biomedical researchers including clinical geneticists, bioinformaticians, researchers working with model organisms, and wet lab scientists researching human physiology at the molecular level in both healthy and disease states. The browser integrates the results of thousands of biomedical labs – including a wide range of biochemical assays, genetic studies, curations, sequencing projects, and computer analyses into a series of tracks aligned to the underlying genomic sequence. The genome provides a natural integration framework for these diverse data sources, which the browser showcases at a variety of display scales ranging from the single base to individual genes, entire chromosomes, and ultimately to the genome as a whole. The Genome Browser is implemented using robust, fast, high-quality software capable of handling over one million hits per day. This web software provides a window into an exceptionally detailed and well-documented database that can be queried computationally as well as browsed graphically. The database is loaded with a suite of programs, developed both at UCSC and elsewhere, capable of distilling huge genomics data sets into high-quality annotations of the genome. Significant engineering effort is invested to ensure the quality of the software and data sets, including those developed by external contributors. The system is designed to make it easy for users to view their own, unpublished, data sets alongside those that we have fully curated and integrated. Consortia and other resources can make their data visible in our browser via “track hubs.” We plan to extend our resource in significant ways. We will help make genomics more equitable to currently underserved populations by moving to a more inclusive “pangenome” reference that includes sequences that represent the greater genomic diversity of humanity, not just samples of convenience from largely European populations. We will enable visualization of individual genomes, not just a single haploid reference genome. We will address the opportunities and challenges of new technologies such as single-cell RNA sequencing and single-molecule long-read DNA sequencing. We will collaborate with others in the increasingly complex ecosystem of biomedical consortia and resources, and will integrate their results into the Genome Browser, and also, through our APIs and our helpful staff, ensure that others can make the best use of data available in their efforts. We will provide tools and data for medical users to understand the significance of sequence variants in the patients they care for and will help characterize regions of greater genomic complexity and medical importance. We will extend our outreach effort to include more online content to help engage a new generation of users.

抽象的 UCSC基因组浏览器和相关工具由数十万生物医学使用包括临床遗传学家，生物信息学家，与模型生物合作的研究人员以及湿实验室的科学家在健康和疾病状态下研究人类生理学的人类生理学。浏览器整合了数千个生物医学实验室的结果 - 包括广泛的生化测定，遗传研究，策展，测序项目和计算机分析分为一系列与之一致的轨道潜在的基因组序列。基因组为这些不同数据提供了自然的整合框架来源，浏览器以各种显示量表的范围从单个基础到单个的各种显示量表基因，整个染色体，最终是整个基因组。基因组浏览器是使用能够处理一个能够处理的强大，快速，高质量软件实现的每天百万击。该网络软件为一个非常详细且有据可查的窗口提供了一个窗口可以在计算上以及图形浏览的数据库。数据库加载了在UCSC和其他地方开发的计划套件，能够将庞大的基因组数据集提炼成基因组的高质量注释。投资了重大的工程工作，以确保软件和数据集，包括外部贡献者开发的软件和数据集。该系统旨在实现它用户易于查看自己的，未发表的数据集以及我们完全策划的数据集，并且融合的。财团和其他资源可以通过“轨道枢纽”在我们的浏览器中可见其数据。我们计划以重要的方式扩展我们的资源。我们将帮助使基因组学更加公平通过移动更具包容性的“ pangenome”参考，包括序列的序列，该序列包括序列代表了人类的更大基因组多样性，而不仅仅是欧洲的便利样本人群。我们将实现各个基因组的可视化，而不仅仅是单倍体参考基因组。我们将解决新技术的机遇和挑战，例如单细胞RNA测序和单分子长读DNA测序。我们将与日益复杂的其他人合作生物医学财团和资源的生态系统，并将其结果整合到基因组浏览器中，而且，通过我们的API和我们的帮助员工，确保其他人可以充分利用可用的数据他们的努力。我们将为医学用户提供工具和数据，以了解序列的重要性他们关心的患者的变体，并将有助于表征具有更大基因组复杂性和医学重要性。我们将扩展我们的外展工作，以包括更多的在线内容，以帮助参与新的内容产生的用户。