Challenges and recommendations to improve the installability and archival stability of omics computational tools

Mangul, Serghei and Mosqueiro, Thiago and Abdill, Richard J. and Duong, Dat and Mitchell, Keith and Sarwal, Varuni and Hill, Brian and Brito, Jaqueline and Littman, Russell Jared and Statz, Benjamin and Lam, Angela Ka-Mei and Dayama, Gargi and Grieneisen, Laura and Martin, Lana S. and Flint, Jonathan and Eskin, Eleazar and Blekhman, Ran (2019) Challenges and recommendations to improve the installability and archival stability of omics computational tools. PLOS Biology, 17 (6). e3000333. ISSN 1545-7885

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Abstract

Developing new software tools for analysis of large-scale biological data is a key component of advancing modern biomedical research. Scientific reproduction of published findings requires running computational tools on data generated by such studies, yet little attention is presently allocated to the installability and archival stability of computational software tools. Scientific journals require data and code sharing, but none currently require authors to guarantee the continuing functionality of newly published tools. We have estimated the archival stability of computational biology software tools by performing an empirical analysis of the internet presence for 36,702 omics software resources published from 2005 to 2017. We found that almost 28% of all resources are currently not accessible through uniform resource locators (URLs) published in the paper they first appeared in. Among the 98 software tools selected for our installability test, 51% were deemed “easy to install,” and 28% of the tools failed to be installed at all because of problems in the implementation. Moreover, for papers introducing new software, we found that the number of citations significantly increased when authors provided an easy installation process. We propose for incorporation into journal policy several practical solutions for increasing the widespread installability and archival stability of published bioinformatics software.

Item Type: Article
Subjects: Lib Research Guardians > Medical Science
Depositing User: Unnamed user with email support@lib.researchguardians.com
Date Deposited: 21 Jan 2023 07:58
Last Modified: 02 Jul 2024 04:01
URI: http://eprints.classicrepository.com/id/eprint/6

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