Does Publicly Funded Research Have to Result in Open Source Code?


A debate is heating up in the academic community over whether software that is generated by publicly funded research must be released with an open source license. The Internet is one example of how releasing research code benefited the public, but the trend seems to be changing now, and universities are more likely to consider the profit opportunity. The Bayh-Dole Act paved the way for the privatization of publicly funded resources, but not everyone is happy with the results.

Against the tide of privatization comes a group of bioinformatics researchers and programmers with an online petition to require that all software created by publicly funded research projects be licensed as open source. They have founded a group and a Web site,, to further this cause.

Here we present two opposing viewpoints on this issue:

O'Reilly Bioinformatics Technology Conference

The authors of both articles will be presenting sessions at the upcoming O'Reilly Bioinformatics Technology Conference.

The Open Informatics Petition is written by Jason E. Stewart and Harry Mangalam, two of the petition's authors, and it explains the rationale behind their efforts. Jason and Harry argue that if the public is paying for the development of software, it should get to use and see the source code, and that making research code available with an open source license is necessary for programs to receive the same type of peer review that scientific papers require.

Why I'm Not Supporting the Open Informatics Petition presents a dissenting viewpoint from Andrew Dalke, a prominent bioinformatics programmer and staunch open source supporter. Andrew explains why he can't support the petition's goal of forcing all code that comes out of publicly funded research to be licensed as open source, even though he is a supporter of open source software and a major contributor to open source bioinformatics projects. Andrew argues that much of the code generated for scientific research is based on previously written, non-open source software, and this requirement would cause a huge amount of this research to be either abandoned or started from scratch.

Give both sides of the argument a read, and let us know where you come down on the issue by adding your comments to the reader-feedback section. This issue stretches far beyond the discipline of bioinformatics, and it's sure to be a lively debate.