Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities
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.
Cite
@article{arxiv.2203.16261,
title = {Packaging, containerization, and virtualization of computational omics methods: Advances, challenges, and opportunities},
author = {Mohammed Alser and Sharon Waymost and Ram Ayyala and Brendan Lawlor and Richard J. Abdill and Neha Rajkumar and Nathan LaPierre and Jaqueline Brito and Andre M. Ribeiro-dos-Santos and Can Firtina and Nour Almadhoun and Varuni Sarwal and Eleazar Eskin and Qiyang Hu and Derek Strong and Byoung-Do and Kim and Malak S. Abedalthagafi and Onur Mutlu and Serghei Mangul},
journal= {arXiv preprint arXiv:2203.16261},
year = {2022}
}