BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
BioShaDock: a community driven bioinformatics shared Docker-based tools registry.
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DOI：
10.12688/f1000research.7536.1
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发表时间：
2015-01-01
期刊：
影响因子：
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通讯作者：
Collin, Olivier
中科院分区：
文献类型：
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作者：
Moreews, Francois;Sallou, Olivier;Collin, Olivier
以Docker为代表的Linux容器技术为科学软件所需的复杂而耗时的安装过程提供了一种替代方案。它们使部署和过程隔离变得容易，以及它们允许跨环境和版本的再现性，是使它们成为生物信息基础设施建设的有趣候选人的品质之一，从单个工作站到高吞吐量计算架构。Docker Hub是一个公共注册中心，可用于将生物信息学软件作为Docker镜像分发。然而，它缺乏管理和通用性，使生物信息学用户很难找到所需的最合适的图像。BioShaDock是一个以生物信息学为中心的Docker注册中心，它提供了一个本地和完全受控的环境来构建和发布生物信息学软件作为可移植的Docker映像。它在身份验证和权限管理方面对Docker注册表进行了许多改进，使其能够集成到现有的生物信息基础设施中，如计算平台。与注册图像相关联的元数据是以领域为中心的，包括例如埃达姆本体中定义的概念，EDAM本体是生物信息学中常用术语的共享和结构化词汇表。注册表还包括用户定义的标签，以方便其发现，以及ELIXIR注册表中工具描述的链接（如果已经存在）。如果没有，BioShaDock注册表将与注册表同步，以根据BioShaDock条目元数据在Elixir注册表中创建新的描述。此链接将帮助用户获得有关该工具的更多信息，例如其埃达姆操作，输入和输出类型。这允许与ELIXIR工具和数据服务注册表集成，从而为生物信息学社区提供此类图像的适当可见性。
Linux container technologies, as represented by Docker, provide an alternative tocomplex and time-consuming installation processes needed for scientific software. The ease of deployment and the process isolation they enable, as well as the reproducibility they permit across environments and versions, are among the qualities that make them interesting candidates for the construction of bioinformatic infrastructures, at any scale from single workstations to high throughput computing architectures. The Docker Hub is a public registry which can be used to distribute bioinformatic software as Docker images. However, its lack of curation and its genericity make it difficult for a bioinformatics user to find the most appropriate images needed. BioShaDock is a bioinformatics-focused Docker registry, which provides a local and fully controlled environment to build and publish bioinformatic software as portable Docker images. It provides a number of improvements over the base Docker registry on authentication and permissions management, that enable its integration in existing bioinformatic infrastructures such as computing platforms. The metadata associated with the registered images are domain-centric, including for instance concepts defined in the EDAM ontology, a shared and structured vocabulary of commonly used terms in bioinformatics. The registry also includes user defined tags to facilitate its discovery, as well as a link to the tool description in the ELIXIR registry if it already exists. If it does not, the BioShaDock registry will synchronize with the registry to create a new description in the Elixir registry, based on the BioShaDock entry metadata. This link will help users get more information on the tool such as its EDAM operations, input and output types. This allows integration with the ELIXIR Tools and Data Services Registry, thus providing the appropriate visibility of such images to the bioinformatics community.