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.

This raises another point that every file must contain a copyright notice, and replacing copyright notices for the GPL with those for CC0 or another license would be rather laborious.

My solution is that authors should absolutely be allowed to keep their own licensing terms upon putting code in Dryad. If they haven’t thought of licensing terms, they should be encouraged to use the GPLv3 or the Apache license (which are compatible with each other).

CC0 is rather restrictive and under this a license I surely would not put any of my code into DRYAD. I would prefer a more liberal system that allows to assign any of the opensource licenses that does not restrict the creator of the software so strongly [Note 3 from the cc0-faq mention that CC0 is compatible with GPL -- I fail to see how that could work].

If I create software and put it under CC0, but keep developing and refining the code, are these extension now under my own copyright or under CC0? How different has derivative work to be to not fall under the license anymore? GPL is rather clear on this, because it “poisons” all derivative work, but allows the original creator the right to assign different licenses, in contrast to CC0 that takes that right away.

Daniel mentions dedicated software repositories that allow a variety of opensource licenses. That sounds superficially very nice, but I always wondered about the long-term perspective. Will github/sourceforge and the like survive the next 20 years? For example, Sourceforge is owned by geeknet, a publicly traded company, if they go under, then what? Would we be OK of the library of congress is run by a private company?

In addition, sourceforge/github represent active projects, it would be nice to have a repository, like DRYAD, that can hold a particular snapshot of a software project.

Peter Beerli

Software in general is probably better hosted in dedicated software repositories, provided they meet some basic long-term preservation criteria. These also typically allow for a wide variety of licenses. The DRYAD entry and/ or the paper describing it could then link there.

If the authors want a DOI for their code, they can choose between putting it under CC0 at DRYAD and submitting it to dedicated journals.

As for supplementary materials, I think CC0 would be an appropriate default, but allowing CC-BY is probably necessary as long as journals have not clarified their policies in this regard.

As a sidenote, I think it would help if you would add a preview option and/ or a list of allowed HTML tags.