TreeBASE and Dryad

It is now generally expected that scientists, unless working on commercial or otherwise confidential projects, make the data underlying their scientific publications freely and publicly available, so that the studies can be replicated if necessary and so that others can use the data for further research.

Sometimes the data are submitted as supplementary material to be published on the journal website, together with the article itself. Some research organisations have their own data repositories. In many cases, however specialised databases are used. GenBank, for example, is a repository of DNA sequence data. Further down the analysis pipeline, I have in the past used TreeBASE to make available sequence alignment matrices and phylogenetic trees, and in one case I have reanalysed other people's data after obtaining them from there.

Recently I had reason to submit another such set of data matrices and phylogenetic trees to a database, and I thought I would go back to TreeBASE. Somehow it did not work out as well as it did a few years ago.

I was able to log in, I created a new submission, I submitted my files, and I described our analysis. The latter process is rather clunky, but okay, it works. Then it turned out that we needed to redo one of the phylogenetic analyses minus one sequence, so I had to delete one of the matrices and one of the trees and replace them with updated versions. That is when the fun started.

Although googling around a bit suggests that other people can do so, I find it impossible to delete anything in TreeBASE. There is no delete button next to anything except co-authors and submissions (i.e. the entire studies). Being unable to change data in a submission, I decided to delete the entire submission and start from scratch. That is surely not how it is meant to work, and it is a lot of extra effort, but what can I do?

As it turns out, not even that. When I ask that a submission be deleted, the web interface thinks for a bit an then throws a Java error at me. I now have three submissions under identical names and cannot delete the first two. Hurray.

At some point I thought I could maybe try out the alternative data repository Dryad.  Perhaps that would work more reliably? At least I have seen it used in several publications lately. I have now twice submitted my eMail address on their 'sign up for a new account' form, been told twice that a confirmation eMail has been sent, and days later neither I nor my spam folder have received any such message.

Perhaps the journal will accept our manuscript without us having the matrix and trees in a public repository? This process is becoming somewhat off-putting.

Update: After a mere four days I have now finally been sent a confirmation link by Dryad. Will see how that repository works.