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Related Experiment Video

Updated: Mar 25, 2026

High-Throughput Transcriptome Analysis for Investigating Host-Pathogen Interactions

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Published on: March 5, 2022

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

François Moreews¹, Olivier Sallou², Hervé Ménager³

¹Genscale team, IRISA, Rennes, France.

|February 26, 2016

Summary

This summary is machine-generated.

BioShaDock offers a curated Docker registry for bioinformatics, simplifying software deployment and enhancing reproducibility. This platform improves upon generic registries by providing domain-specific metadata and seamless integration with ELIXIR for better tool discovery.

Keywords:

bioinformatics community driven registry container deployment docker interoperability maintainability

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Area of Science:

Bioinformatics
Computational Biology
Software Engineering

Background:

Scientific software installation is often complex and time-consuming.
Linux container technologies like Docker offer solutions for deployment, isolation, and reproducibility.
Existing public Docker registries lack curation, making bioinformatics tool discovery difficult.

Purpose of the Study:

To introduce BioShaDock, a bioinformatics-specific Docker registry.
To address the limitations of generic Docker registries for scientific software.
To improve the discoverability and integration of bioinformatics tools.

Main Methods:

Developed a local, controlled Docker registry environment for building and publishing bioinformatics software.
Implemented enhanced authentication and permissions management for infrastructure integration.
Utilized domain-centric metadata, including EDAM ontology concepts, and user-defined tags for improved searchability.
Integrated with the ELIXIR registry to link Docker images with tool descriptions and operations.

Main Results:

BioShaDock provides a curated and controlled environment for bioinformatics Docker images.
Enhanced metadata and tagging facilitate easier discovery of relevant bioinformatics tools.
Integration with ELIXIR ensures comprehensive tool information and visibility within the bioinformatics community.

Conclusions:

BioShaDock significantly improves the management and accessibility of bioinformatics software via Docker images.
The platform enhances reproducibility and simplifies the deployment of complex bioinformatic infrastructures.
BioShaDock fosters better integration and visibility of bioinformatics tools through its specialized features and ELIXIR linkage.