The UCSC Genome Browser

UCSC 基因组浏览器

• 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
• 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

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被数十万生物医学工作者使用 研究人员，包括临床遗传学家、生物信息学家、研究模式生物的研究人员，以及 湿实验室科学家在健康和疾病状态的分子水平上研究人体生理学。这 浏览器集成了数千个生物医学实验室的结果 - 包括广泛的生化测定， 基因研究、策划、测序项目和计算机分析成一系列与 基础基因组序列。基因组为这些不同的数据提供了一个自然的整合框架 源，浏览器以各种显示比例展示，从单一基地到单独基地 基因、整个染色体，最终到整个基因组。 基因组浏览器是使用强大、快速、高质量的软件实现的，能够处理超过一个 每天百万次点击。该网络软件提供了一个了解异常详细且记录齐全的信息的窗口 可以通过计算方式查询以及通过图形方式浏览的数据库。数据库加载了一个 UCSC 和其他地方开发的程序套件，能够将巨大的基因组数据集提炼成 基因组的高质量注释。投入了大量的工程工作来确保质量 软件和数据集，包括外部贡献者开发的软件和数据集。该系统的设计目的是使其 用户可以轻松查看自己的、未发布的数据集以及我们完全策划和发布的数据集 融合的。联盟和其他资源可以通过“跟踪中心”在我们的浏览器中显示其数据。 我们计划以重大方式扩展我们的资源。我们将帮助基因组学变得更加公平 通过转向更具包容性的“泛基因组”参考，其中包括以下序列，来解决服务不足的人群 代表了人类更大的基因组多样性，而不仅仅是来自大部分欧洲人的方便样本 人口。我们将实现单个基因组的可视化，而不仅仅是单个单倍体参考基因组。 我们将应对单细胞RNA测序等新技术带来的机遇和挑战 单分子长读DNA测序。我们将在日益复杂的情况下与其他人合作 生物医学联盟和资源的生态系统，并将其结果整合到基因组浏览器中， 此外，通过我们的 API 和乐于助人的员工，确保其他人可以充分利用可用的数据 他们的努力。我们将为医疗用户提供工具和数据来理解序列的意义 他们所照顾的患者中的变异将有助于表征基因组复杂性更高的区域 医学重要性。我们将扩大外展工作，纳入更多在线内容，以帮助吸引新的人 一代用户。