Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities

Mohammed Alser; Sharon Waymost; Ram Ayyala; Brendan Lawlor; Richard J. Abdill; Neha Rajkumar; Nathan LaPierre; Jaqueline Brito; Andre M. Ribeiro-dos-Santos; Can Firtina; Nour Almadhoun; Varuni Sarwal; Eleazar Eskin; Qiyang Hu; Derek Strong; Byoung-Do; Kim; Malak S. Abedalthagafi; Onur Mutlu; Serghei Mangul

arXiv · 2203.16261

Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities

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Abstract

Omics software tools have reshaped the landscape of modern biology and become an essential component of biomedical research. The increasing dependence of biomedical scientists on these powerful tools creates a need for easier installation and greater usability. Packaging, virtualization, and containerization are different approaches to satisfy this need by wrapping omics tools in additional software that makes the omics tools easier to install and use. Here, we systematically review practices across prominent packaging, virtualization, 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 packaging, virtualization, and containerization of omics software more sustainable and robust to increase the reproducibility of biomedical and life science research.

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Mohammed Alser, Sharon Waymost, Ram Ayyala, Brendan Lawlor, Richard J. Abdill, Neha Rajkumar, Nathan LaPierre, Jaqueline Brito, Andre M. Ribeiro-dos-Santos, Can Firtina, Nour Almadhoun, Varuni Sarwal, Eleazar Eskin, Qiyang Hu, Derek Strong, Byoung-Do, Kim, Malak S. Abedalthagafi, Onur Mutlu, Serghei Mangul. 2022-03-30. Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities. https://arxiv.org/abs/2203.16261

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