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CREDO: a friendly Customizable, REproducible, DOcker file generator for bioinformatics applications.

Simone Alessandri1, Maria L Ratto2, Sergio Rabellino3

  • 1Polytechnic of Turin, Turin, Italy.

BMC Bioinformatics
|March 13, 2024
PubMed
Summary

CREDO is a new tool that generates Dockerfiles for bioinformatics, simplifying the creation of reproducible research environments. This enhances the reliability and efficiency of complex biological data analysis.

Keywords:
BioinformaticsDockerOpen scienceReproducibilitySoftware sharing

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Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • Reproducibility in bioinformatics is challenged by inconsistent analysis methods and lack of standardization.
  • This leads to result discrepancies, impacting research credibility and fostering mistrust.
  • Open science practices, including data and code sharing, are encouraged to mitigate these issues.

Purpose of the Study:

  • To introduce CREDO, a Customizable, REproducible, DOcker file generator.
  • To address reproducibility challenges in bioinformatics research through automated Docker container generation.
  • To promote efficient and reliable bioinformatics analysis.

Main Methods:

  • CREDO generates Docker containers with embedded bioinformatics tools.
  • It simplifies Dockerfile creation by managing heterogeneous packages (e.g., Bioconductor, Conda).
  • Package information and dependencies are stored in a GitHub-compatible format for reproducibility.

Main Results:

  • CREDO facilitates the building and distribution of Docker images for bioinformatics applications.
  • It streamlines the generation of Docker images, enhancing research reproducibility.
  • The tool offers a user-friendly GUI and generates modular Docker images.

Conclusions:

  • CREDO is a valuable tool for improving reproducibility in bioinformatics.
  • It supports efficient Docker image creation for life scientists.
  • The tool promotes open science practices and enhances the reliability of bioinformatics research.