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From Voxels to Knowledge: A Practical Guide to the Segmentation of Complex Electron Microscopy 3D-Data

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Packaging and containerization of computational methods.

Mohammed Alser¹, Brendan Lawlor^2,3, Richard J Abdill⁴

¹Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.

Nature Protocols

|April 2, 2024

Summary

This summary is machine-generated.

Omics data analysis software is complex. Packaging and containerization simplify installation and usability for researchers, improving reproducibility in biomedical research.

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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.