Software in the Scientific Literature: Problems with Seeing, Finding, and Using Software Mentioned in the Biology Literature James Howison School of Information, University of Texas at Austin, 1616 Guadalupe Street, Austin, TX 78701, USA. E-mail:
[email protected] Julia Bullard School of Information, University of Texas at Austin, 1616 Guadalupe Street, Austin, TX 78701, USA. E-mail:
[email protected] Software is increasingly crucial to scholarship, yet the incorporates key scientific methods; increasingly, software visibility and usefulness of software in the scientific is also key to work in humanities and the arts, indeed to work record are in question. Just as with data, the visibility of with data of all kinds (Borgman, Wallis, & Mayernik, 2012). software in publications is related to incentives to share software in reusable ways, and so promote efficient Yet, the visibility of software in the scientific record is in science. In this article, we examine software in publica- question, leading to concerns, expressed in a series of tions through content analysis of a random sample of 90 National Science Foundation (NSF)- and National Institutes biology articles. We develop a coding scheme to identify of Health–funded workshops, about the extent that scientists software “mentions” and classify them according to can understand and build upon existing scholarship (e.g., their characteristics and ability to realize the functions of citations. Overall, we find diverse and problematic Katz et al., 2014; Stewart, Almes, & Wheeler, 2010). In practices: Only between 31% and 43% of mentions particular, the questionable visibility of software is linked to involve formal citations; informal mentions are very concerns that the software underlying science is of question- common, even in high impact factor journals and across able quality.