The open source programming languages, often with a bio-suffix, i.e. BioPerl, BioJava, and BioRuby, have been widely used in bio informatics and computational biology research. The computational tools written in these languages provide multiple functionalities as the languages make them flexible to create customized analysis and examination of biological data. In this paper, we investigate one of the software quality parameters, " maintainability", in BioPerl, BioJava, and BioRuby projects using comment density metric in their source code repositories. Furthermore, we evaluate the "popularity" of these three languages in bioinformatics communities using three other software metrics such as number of committers, commit frequency, and lines of code. To perform this study, source code repositories of these three open source projects have been analyzed from the first release, which covers all the programming activities of the projects from the starting date until July 2011. Our results show BioPerl to be the most popular language among the three languages in open source communities. In addition, investigation on comment density of these three open source projects has shown that BioPerl is the most promising one in terms of future maintainability and quality of the project. The results of this research can be useful for developers in choosing an appropriate language for the development of bioinformatics applications. © 2012 Published by Elsevier Ltd.
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