Packaging and containerization of computational methods

Mohammed Alser¹, Brendan Lawlor^{2

3}, Richard J Abdill⁴, Sharon Waymost⁵, Ram Ayyala^{6

7}, Neha Rajkumar⁸, Nathan LaPierre^{5

9}, Jaqueline Brito⁷, André M Ribeiro-Dos-Santos¹⁰, Nour Almadhoun¹, Varuni Sarwal⁵, Can Firtina¹, Tomasz Osinski¹¹, Eleazar Eskin^{5

12

13}, Qiyang Hu¹⁴, Derek Strong¹¹, Byoung-Do B D Kim¹¹, Malak S Abedalthagafi^{15

16}, Onur Mutlu¹, Serghei Mangul^{17

18}

Affiliations

¹ Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
² Department of Computer Science, Munster Technological University, Cork, Ireland.
³ Department of Biological Sciences, Munster Technological University, Cork, Ireland.
⁴ Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
⁵ Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
⁶ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
⁷ Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
⁸ Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.
⁹ Department of Human Genetics, University of Chicago, Chicago, IL, USA.
¹⁰ Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
¹¹ Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA.
¹² Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
¹³ Department of Human Genetics, University of California, Los Angeles, CA, USA.
¹⁴ Office of Advanced Research Computing, University of California, Los Angeles, CA, USA.
¹⁵ Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA.
¹⁶ King Salman Center for Disability Research, Riyadh, Saudi Arabia.
¹⁷ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.
¹⁸ Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.

PMID: 38565959
DOI: 10.1038/s41596-024-00986-0

Packaging and containerization of computational methods

Mohammed Alser et al. Nat Protoc. 2024 Sep.

. 2024 Sep;19(9):2529-2539.

doi: 10.1038/s41596-024-00986-0. Epub 2024 Apr 2.

Authors

Affiliations

¹ Department of Information Technology and Electrical Engineering, ETH Zürich, Zurich, Switzerland.
² Department of Computer Science, Munster Technological University, Cork, Ireland.
³ Department of Biological Sciences, Munster Technological University, Cork, Ireland.
⁴ Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, IL, USA.
⁵ Department of Computer Science, University of California, Los Angeles, Los Angeles, CA, USA.
⁶ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA.
⁷ Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA.
⁸ Department of Bioengineering, University of California, Los Angeles, Los Angeles, CA, USA.
⁹ Department of Human Genetics, University of Chicago, Chicago, IL, USA.
¹⁰ Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY, USA.
¹¹ Center for Advanced Research Computing, University of Southern California, Los Angeles, CA, USA.
¹² Department of Computational Medicine, University of California, Los Angeles, Los Angeles, CA, USA.
¹³ Department of Human Genetics, University of California, Los Angeles, CA, USA.
¹⁴ Office of Advanced Research Computing, University of California, Los Angeles, CA, USA.
¹⁵ Department of Pathology & Laboratory Medicine, Emory University Hospital, Atlanta, GA, USA.
¹⁶ King Salman Center for Disability Research, Riyadh, Saudi Arabia.
¹⁷ Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.
¹⁸ Titus Family Department of Clinical Pharmacy, USC Alfred E. Mann School of Pharmacy and Pharmaceutical Sciences, University of Southern California, Los Angeles, CA, USA. serghei.mangul@gmail.com.

PMID: 38565959
DOI: 10.1038/s41596-024-00986-0

Abstract

Methods for analyzing the full complement of a biomolecule type, e.g., proteomics or metabolomics, generate large amounts of complex data. The software tools used to analyze omics data have reshaped the landscape of modern biology and become an essential component of biomedical research. These tools are themselves quite complex and often require the installation of other supporting software, libraries and/or databases. A researcher may also be using multiple different tools that require different versions of the same supporting materials. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging and containerization are different approaches to satisfy this need by delivering omics tools already wrapped in additional software that makes the tools easier to install and use. In this systematic review, we describe and compare the features of prominent packaging and containerization platforms. We outline the challenges, advantages and limitations of each approach and some of the most widely used platforms from the perspectives of users, software developers and system administrators. We also propose principles to make the distribution of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

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References

1. Alser, M. et al. Technology dictates algorithms: recent developments in read alignment. Genome Biol. 22, 249 (2021). - DOI - PubMed - PMC
1. Mangul, S. et al. Systematic benchmarking of omics computational tools. Nat. Commun. 10, 1393 (2019). - DOI - PubMed - PMC
1. Alser, M., Eudine, J. & Mutlu, O. Genome-on-diet: taming large-scale genomic analyses via sparsified genomics. Preprint at arXiv https://doi.org/10.48550/arXiv.2211.08157 (2022).
1. Meyer, F. et al. Critical assessment of metagenome interpretation: the second round of challenges. Nat. Methods 19, 429–440 (2022). - DOI - PubMed - PMC
1. Cox, R. Surviving software dependencies. Commun. ACM 62, 36–43 (2019). - DOI

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Packaging and containerization of computational methods

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Packaging and containerization of computational methods

Authors

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Abstract

References

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MeSH terms

Grants and funding

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Full Text Sources