Source code repositories in the journal <i>Bioinformatics</i>.

Here the term “repository” refers to online code hosting services. The journal Bioinformatics publishes new developments in bioinformatics and computational biology. If a paper focuses on software development, authors are required to state software availability in the abstract, including the complete URL [15]. URLs for software hosted on the popular services GitHub, Bitbucket, and SourceForge contain the respective repository name except in rare cases of developers referring to the repository from a different URL or page. The figure shows the results of PubMed searches for the repository names in the title or abstract of papers published in Bioinformatics between 2009 and 2017. The category “Abstracts with none of these” captures all remaining articles published in Bioinformatics for the year, and likely includes many software projects hosted on organization websites or featuring their own domain name, as well as any articles that did not publish software.