The UCSC Genome Browser

摘要 UCSC基因组浏览器和相关工具由数十万生物医学人员使用 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 湿实验室科学家在分子水平上研究健康和疾病状态下的人类生理学。这个 Browser集成了数千个生物医学实验室的结果-包括广泛的生化分析， 基因研究、策展、测序项目和计算机分析到一系列与 潜在的基因组序列。基因组为这些不同的数据提供了一个自然的整合框架 来源，浏览器以从单个基数到单个基数的各种显示比例显示 基因，整个染色体，并最终到达基因组作为一个整体。 Genome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 每天有一百万的点击量。该Web软件提供了一个窗口，让您可以了解非常详细和有良好记录的 既可以通过计算方式查询，也可以通过图形方式浏览的数据库。该数据库加载了一个 UCSC和其他地方开发的一套程序，能够将巨大的基因组数据集提炼成 高质量的基因组注释。投入了大量的工程工作以确保 软件和数据集，包括由外部贡献者开发的软件和数据集。该系统的设计目的是让它 用户可以轻松查看自己未发布的数据集，以及我们已完全管理和 集成的。财团和其他资源可以通过“跟踪中心”在我们的浏览器中查看他们的数据。 我们计划以重大的方式扩展我们的资源。我们将帮助使基因组学对当前更加公平 服务不足的人群，通过转向包含以下序列的更具包容性的Pangenome参考 代表着人类更大的基因组多样性，而不仅仅是主要来自欧洲的便利样品 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。 我们将应对新技术的机遇和挑战，如单细胞RNA测序和 单分子长读DNA测序。我们将与其他人在日益复杂的 生物医学联盟和资源的生态系统，并将把他们的结果整合到基因组浏览器中， 此外，通过我们的API和我们乐于助人的员工，确保其他人可以最好地利用 他们的努力。我们将为医疗用户提供工具和数据，让他们了解序列的意义 他们所关心的患者中的变异，并将有助于表征基因组更复杂的区域和 医学上的重要性。我们将扩大我们的外展努力，包括更多在线内容，以帮助参与新的 新一代用户。

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 The system is designed to make it easy for users to view their own, unpublished, data sets alongside those that we have fully curated and integrated.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.