BioShaDock: a community driven bioinformatics shared Docker-based tools registry

Abstract

Linux container technologies, as represented by Docker, provide an alternative to complex 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.

The Dockstore: enabling modular, community-focused sharing of Docker-based genomics tools and workflows

“…A number of existing projects, such as BioShaDock 7 , Bioboxes 8 , and BioDocker ( http://biodocker.org), focus on encapsulating bioinformatics tools in Docker images in a way similar to Dockstore. BioDocker encourages the use of bioinformatics tools in Docker images by curating them in a single GitHub repository that collaborators can contribute to.…”

The Experiment Factory: Reproducible Experiment Containers

“…n.d.), Baker (n.d.), Open Science Collaboration (2015)) has been well met by many efforts (Belmann et al 2015, Moreews et al (2015, Boettiger (2014), Santana-Perez and Pérez-Hernández (2015), Wandell et al (2015)) across scientific disciplines to capture dependencies required for a scientific analysis. Behavioral research is especially challenging, historically due to the need to bring a study participant into the lab, and currently due to needing to develop and validate a well-tested set of paradigms.…”

Robust Cross-Platform Workflows: How Technical and Scientific Communities Collaborate to Develop, Test and Share Best Practices for Data Analysis

“…When combined with lightweight containers such as Docker or Singularity, the recipe becomes directly installable (Fig. 2) [28]. It needs to be left to the users' opinion where to draw the line between traditional distribution-provided packages that are already used to communicate with the kernel and the end-user packages of the given scientific discipline, which are often redundantly available from the Linux distribution and a Linuxbrew/Bioconda community, or other repositories like Bioconductor [9] (http://bio conductor.org).…”