Thanks for your comment.

Peggy Schaeffer, Dryad Communications Coordinator

“JISC is already acting on a number of the recommendations – including funding the Dryad project mentioned in the report. Dryad-UK provides a repository for the data underpinning research articles, encouraging greater research openness. The BMJ Open journal and titles from BioMedCentral and PLoS have become partners, integrating their submission process with Dryad and strongly encouraging authors to deposit research data.”

As far as relying on software repositories, I think this is risky. What are the long term guarantees that they will stay up? Even if, say, sourceforge as a whole remains up, there’s a chance that individual projects can die. I know both sourceforge and Google Code allow project names to be taken over by new projects [I've actually done this, in one case]: they typically require evidence that the other project is dead and has little product, but that’s a decision up to staff at each site. A project that consists of a few scripts done by a grad student who moves on to other things might have important code for our community but might not be seen as critically important by a sourceforge admin.

I also think it’s important to save the state of the code at the time of publication, rather than pointing to its current version. Software has bugs — it’s critical to be able to see if a paper’s conclusions come from a bug in the software, and this is harder to do if we’re just pointed to the current version (unless you start doing other add ons like requiring storing of commit numbers or other detailed info about the version of the software used in the paper).

A final point: software is a key ingredient to many studies, but it is ephemeral (for example, Mark Pagel’s classic Continuous program is no longer available for download from his website, though its functions are in another program). It is thus important that software find a home in Dryad.