Dockstore: The Community Platform for Reproducible Biomedical Workflows and Applications

Dockstore：可重复的生物医学工作流程和应用程序的社区平台

• 批准号: 10491075
• 负责人: Benedict Paten
• 金额: $ 106.77万
• 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: 2021-09-20 至 2026-06-30
• 项目状态: 未结题
• 来源: https://reporter.nih.gov/project-details/10491075
• 关键词: Address; Adopted; Agreement; Atlases; Authorization documentation; Biological; Cells; Cloud Computing; Code; Collaborations; Communities; Complex; Computational Science; Computer Analysis; Computing Methodologies; Consensus; Data Set; Development; Ecosystem; Education and Outreach; Educational workshop; Ensure; Environment; FAIR principles; Feedback; Foundations; Funding; Generations; Genomics; Goals; Grant; Growth and Development function; Health; Human; Infrastructure; Language; Learning; Link; Metadata; Methods; Morphologic artifacts; National Human Genome Research Institute; Nature; Operating System; Peer Review; Persons; Publications; Publishing; Publishing Peer Reviews; Reproducibility; Reproduction; Resources; Running; Science; Secure; Series; Services; System; Testing; Training; Trust; U-Series Cooperative Agreements; Work; base; chain of trust; cloud platform; computational platform; computerized tools; digital object identifier; improved; infrastructure development; laptop; open source; peer; programs; rapid growth; repository; social; software development; tool; web app; webinar

Dockstore - A Platform for Creating, Sharing, Publishing and Reproducing Computational Science For science to work analyses, tools and workflows must be reproducible; reproduction is essential to building consensus and confidence, and improving the state of the art. A large and growing set of scientific methods are computational in nature, and we can make these computational methods exactly reproducible. Dockstore is a repository for scientific tools and workflows that provides the means precisely to capture the code, parameters and operating system environment that are necessary. For tool users it makes it easy to find a given tool and then run it precisely as the author intended. It is possible to export a tool for use in a cloud platform, such as NHGRI AnVIL, with a few clicks, or similarly easily download it to an institutional compute environment, or even a laptop. For tool creators it provides an integrated system to publish versioned scientific tools with a citable Digital Object Identifier (DOI), linking to containers, existing code repositories and capturing vital parameter configuration information. Dockstore, previously funded by an R01 from NHGRI grant, has grown tremendously over the last four years. It now has thousands of users, hosts hundreds of tools and workflows, and is used as the methods for multiple major platforms and projects. Though not technically a renewal, this proposal would provide the core funding to continue the development and growth of Dockstore, which is a fully open source platform entirely reliant on grant funding. This proposal would grow Dockstore as a resource to make it a hub for broadly sharing computational science. The aims of the proposal cover foundational infrastructure development (Aim 1), support for sharing new, popular content types (Aim 2), the expansion of publishing features to make Dockstore more broadly useful (Aim 3), and a strong focus on training and outreach (Aim 4). The infrastructure development of Aim 1 will increase the scaling and robustness of Dockstore and support Dockstore as a secure, compliant resource, enabling it to safely host pre-publication tools and workflows working with managed access datasets. It will integrate Dockstore more deeply with secure cloud platforms, such as the NHGRI AnVIL. The expansion of content types by Aim 2 will, for example, make it possible to publish programming notebooks on Dockstore. Such artifacts are widely used but not yet robustly searchable by any scientific resource. Aim 3 will bring ORCID integration, allowing users to authenticate themselves and then sign and endorse their work, and to provide open peer review of published tools. Aim 4 will focus on growing and educating the user base via an expansion of online training material, webinars, in person workshops and collaborations with training for partner projects using Dockstore. We will also further develop means to continuously acquire user feedback.

Dockstore - 一个创建、共享、发布和复制计算科学的平台 为了让科学发挥作用，分析、工具和工作流程必须是可重复的；繁殖对于建筑至关重要 共识和信心，并提高技术水平。大量且不断增长的科学方法 本质上是计算性的，我们可以使这些计算方法完全可重现。坞站是 科学工具和工作流程的存储库，提供精确捕获代码的方法， 必要的参数和操作系统环境。对于工具用户来说，可以轻松找到 给定工具，然后按照作者的意图精确地运行它。可以导出在云中使用的工具 只需点击几下即可轻松将其下载到机构计算平台，例如 NHGRI AnVIL 环境，甚至笔记本电脑。对于工具创建者，它提供了一个集成系统来发布版本化的科学 具有可引用的数字对象标识符（DOI）的工具，链接到容器、现有代码存储库并捕获 重要参数配置信息。 Dockstore 之前由 NHGRI 的 R01 拨款资助，在过去四年中取得了巨大的发展 年。它现在拥有数千名用户，托管数百个工具和工作流程，并被用作 多个主要平台和项目。虽然从技术上讲不是更新，但该提案将提供核心 为 Dockstore 的继续开发和成长提供资金，Dockstore 是一个完全开源的平台 依赖赠款资金。 该提案将使 Dockstore 发展成为一种资源，使其成为广泛共享计算的中心 科学。该提案的目标包括基础设施发展（目标 1）、支持共享 新的、流行的内容类型（目标 2），扩展发布功能以使 Dockstore 更广泛 有用（目标 3），并高度重视培训和推广（目标 4）。目标1的基础设施发展 将提高 Dockstore 的可扩展性和稳健性，并支持 Dockstore 作为安全、合规的资源， 使其能够安全地托管使用托管访问数据集的预发布工具和工作流程。它将 将 Dockstore 与安全云平台（例如 NHGRI AnVIL）更深入地集成。的扩展 例如，Aim 2 的内容类型将使在 Dockstore 上发布编程笔记本成为可能。 此类人工制品被广泛使用，但尚未通过任何科学资源进行可靠的搜索。目标3将带来 ORCID 集成，允许用户验证自己的身份，然后签署和认可他们的工作，并 对已发布的工具提供公开的同行评审。目标 4 将重点通过以下方式发展和教育用户群： 扩大在线培训材料、网络研讨会、面对面研讨会以及与培训合作 使用 Dockstore 的合作伙伴项目。我们还将进一步开发持续获取用户反馈的手段。