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: 10269187
• 负责人: Brian O'Connor
• 金额: $ 109.32万
• 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/10269187
• 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、出版和复制计算科学的平台 对于科学来说，分析、工具和工作流程必须是可复制的；复制是构建 共识和信心，提高艺术水平。一套庞大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精确地重现。码头商店是 科学工具和工作流程的存储库，提供准确捕获代码的手段， 必要的参数和操作系统环境。对于工具用户来说，它可以很容易地找到 给出工具，然后精确地按照作者的意图运行它。可以导出工具以在云中使用 平台，例如NHGRI砧板，只需点击几下，或者类似地轻松地将其下载到机构计算机 环境，甚至是笔记本电脑。对于工具创建者，它提供了一个集成的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)、链接到容器、现有代码库和捕获的工具 重要参数配置信息。 Dockstore之前是由NHGRI拨款的R01资助的，在过去的四年里增长了很快 好几年了。它现在拥有数千名用户，托管数百个工具和工作流，并用作 多个重大平台和项目。虽然从技术上讲不是续签，但这项提案将提供核心 为继续发展和壮大Dockstore提供资金，Dockstore是一个完全开放源代码的平台 依靠赠款资助。 这项提议将把Dockstore发展为一种资源，使其成为广泛共享计算资源的中心 科学。该提案的目标包括基础设施发展(目标1)、支持共享 新的流行内容类型(目标2)，发布功能的扩展使Dockstore变得更广泛 有用(目标3)，高度重视培训和外联(目标4)。目标1的基础设施发展 将提高Dockstore的可扩展性和稳定性，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Access数据集的发布前工具和工作流。会的 将Dockstore与安全的云平台(如NHGRI铁锤)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。 这类文物被广泛使用，但还不能被任何科学资源有力地搜索到。目标3将带来 ORCID集成，允许用户验证自己，然后签署和认可他们的工作，并 对已发布的工具提供开放的同行评审。目标4将专注于通过 扩展在线培训材料、网络研讨会、面对面研讨会以及与以下培训的协作 使用Dockstore的合作伙伴项目。我们还将进一步开发手段，不断收集用户反馈。