PT  - JOURNAL ARTICLE
AU  - Serghei Mangul
AU  - Thiago Mosqueiro
AU  - Richard J. Abdill
AU  - Dat Duong
AU  - Keith Mitchell
AU  - Varuni Sarwal
AU  - Brian Hill
AU  - Jaqueline Brito
AU  - Russell Jared Littman
AU  - Benjamin Statz
AU  - Angela Ka-Mei Lam
AU  - Gargi Dayama
AU  - Laura Grieneisen
AU  - Lana S. Martin
AU  - Jonathan Flint
AU  - Eleazar Eskin
AU  - Ran Blekhman
TI  - Challenges and recommendations to improve installability and archival stability of omics computational tools
AID  - 10.1101/452532
DP  - 2019 Jan 01
TA  - bioRxiv
PG  - 452532
4099  - http://biorxiv.org/content/early/2019/05/14/452532.short
4100  - http://biorxiv.org/content/early/2019/05/14/452532.full
AB  - 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 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 due to 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.