Dockstore: The Community Platform for Reproducible Biomedical Workflows and Applications

Dockstore -一个创造、分享、出版和复制计算科学的平台 为了让科学能够进行分析，工具和工作流程必须是可复制的;复制对于构建 共识和信心，并提高艺术的状态。一个大的和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重现。码头商店是 一个科学工具和工作流的存储库，提供精确捕获代码的方法， 参数和操作系统环境是必要的。对于工具用户来说， 给定的工具，然后按照作者的意图运行它。可以导出工具以在云中使用 平台，如NHGRI AnVIL，只需点击几下，或类似地轻松下载到机构计算机 环境，甚至是笔记本电脑。对于工具创建者来说，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，现有代码存储库和捕获 重要参数配置信息。 Dockstore以前由NHGRI赠款的R 01资助，在过去的四年中发展迅速。 年它现在拥有数千名用户，托管数百种工具和工作流，并被用作 多个大型平台和项目。虽然从技术上讲不是一个更新，但这一建议将提供核心 资助继续Dockstore的发展和增长，这是一个完全开源的平台 依靠补助金 这项提议将使Dockstore成为一种资源，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、流行的内容类型（目标2），发布功能的扩展使Dockstore更广泛 有用（目标3），并大力注重培训和推广（目标4）。目标1的基础设施发展 将增加Dockstore的可扩展性和健壮性，并支持Dockstore作为安全，兼容的资源， 使其能够安全地托管使用托管访问数据集的出版前工具和工作流。它将 将Dockstore与安全云平台（如NHGRI AnVIL）更深入地集成。扩大 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。 这些人工制品被广泛使用，但尚未被任何科学资源强大地搜索到。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， 对已发布的工具进行公开的同行评审。Aim 4将专注于通过 扩大在线培训材料、网络研讨会、现场讲习班以及与培训机构的合作， 使用Dockstore的合作伙伴项目。我们还将进一步开发不断获取用户反馈的方法。

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.