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A Bioinformatics Pipeline for Investigating Molecular Evolution and Gene Expression using RNA-seq

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Published on: May 28, 2021

Recommendations for the packaging and containerizing of bioinformatics software.

Bjorn Gruening¹, Olivier Sallou², Pablo Moreno³

¹Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, 79110, Germany.

|September 27, 2019

Summary

Software containers streamline scientific software development and deployment for researchers. The BioContainers Community offers recommendations for standardized bioinformatics packages to enhance software reusability and transparency.

Keywords:

best practices bioinformatics containers and packages reproducibility

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Area of Science:

Computational Biology
Bioinformatics
Scientific Software Engineering

Background:

Software containers revolutionize scientific software development, deployment, and exchange.
They enable easier installation, version management, and pipeline integration for bioinformatics tools.
Standardization is crucial for containerized software to ensure reusability, compatibility, and workflow integration.

Purpose of the Study:

To present a set of recommendations for producing standardized bioinformatics packages and containers.
To provide practical guidelines for improving the discoverability, reusability, and transparency of bioinformatics software.
To guide developers, organizations, journals, and funders in enhancing research software quality and sustainability.

Main Methods:

Development of recommendations by the BioContainers Community.
Focus on practical guidelines for package and container standardization.
Inclusion of aspects for discoverability, reusability, and transparency.

Main Results:

A comprehensive set of recommendations for standardized bioinformatics containers.
Guidelines promoting software discoverability and transparency.
Framework to improve the sustainability of research software.

Conclusions:

Standardized bioinformatics containers are essential for reproducible and efficient research.
The BioContainers Community's recommendations facilitate better integration and usability of scientific software.
Adoption of these guidelines will enhance the overall quality and long-term value of research software.