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Packaging and containerization of computational methods
Mohammed Alser1, Brendan Lawlor2,3, Richard J Abdill4
1Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
Nature Protocols
|April 2, 2024
Summary
Omics data analysis software is complex. Packaging and containerization simplify installation and usability for researchers, improving reproducibility in biomedical research.
Area of Science:
- Biomedical Informatics
- Computational Biology
- Bioinformatics
Background:
- Omics data analysis (e.g., proteomics, metabolomics) generates complex datasets.
- Specialized software tools are essential for modern biomedical research but often have complex installation requirements.
- Dependencies on multiple software versions hinder usability and reproducibility.
Purpose of the Study:
- To systematically review and compare packaging and containerization platforms for omics software.
- To evaluate the challenges, advantages, and limitations of these approaches for users, developers, and administrators.
- To propose principles for sustainable and robust omics software distribution.
Main Methods:
- Systematic review of prominent packaging and containerization platforms.
- Comparative analysis of features, usability, and installation complexity.
- Evaluation from multiple stakeholder perspectives (users, developers, administrators).
Main Results:
- Packaging and containerization offer solutions for omics software installation and usability.
- Different platforms present unique challenges and benefits.
- Key considerations for users, developers, and system administrators were identified.
Conclusions:
- Packaging and containerization enhance the accessibility and usability of omics analysis tools.
- Standardized distribution principles can improve software sustainability and research reproducibility.
- Adoption of these approaches is crucial for advancing biomedical and life science research.
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