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choderalab / ensembler

Automated omics-scale protein modeling and simulation setup.
http://ensembler.readthedocs.io/
GNU General Public License v2.0
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Link to example dataset doesn't work #69

Open rafwiewiora opened 8 years ago

rafwiewiora commented 8 years ago

This is probably not meant to be like this, so pointing out:

* See the example dataset from [modeling all human tyrosine kinases](http://datadryad.org/review?doi=doi:10.5061/dryad.7fg32).

in README.MD gives this:

messages image 29891914 copy
sonyahanson commented 8 years ago

It says Content restricted ahead of article publication, which I think is correct. The article has not been published outside bioRxiv yet, I believe.

jchodera commented 8 years ago

It was accepted, so we should let them know to release this.

@danielparton, any idea how to do this?

danielparton commented 8 years ago

But the article is not actually published yet is it?

On Mon, Apr 4, 2016 at 8:33 PM, John Chodera notifications@github.com wrote:

It was accepted, so we should let them know to release this.

@danielparton, any idea how to do this?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/choderalab/ensembler/issues/69#issuecomment-205560260

jchodera commented 8 years ago

Proofs have been sent in.

danielparton commented 8 years ago

I don't think I have any control over it through their website, but you could contact Dryad and ask if they can make the data available now the proofs have been sent in. I have a feeling they will say no. This would mean Dryad is not suitable if we want to keep a dataset available throughout the whole pre- and post-publication process.

On Mon, Apr 4, 2016 at 9:09 PM, John Chodera notifications@github.com wrote:

Proofs have been sent in.

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/choderalab/ensembler/issues/69#issuecomment-205570555

rafwiewiora commented 8 years ago

I see - well I just thought it strange for our lab to be restricting a dataset - why not have it available pre-publication?

danielparton commented 8 years ago

It's Dryad's policy, not ours - I'm not sure why they have that policy. Maybe they think most researchers don't want to make their data available until the paper is completely published. Or maybe they're worried about changes (e.g. article title) which can happen shortly before publication. Shouldn't be a problem really, but maybe they just haven't built in the capability to automate this. Their upload infrastructure was not exactly super streamlined. See this quote from the FAQ ("What happens to data after it is submitted"):

The data package is publicly released once the online version of the associated publication is available (unless an alternative release option has been selected). Since paper titles, abstracts, authors etc. often change during the publication process, Dryad confirms and updates this information against the accepted/published article.

We weren't really aware of this when we decided to use Dryad. Or at least we hadn't considered what would happen in the period between acceptance and publication. So you guys might want to revisit how you make publication data available in the future, if Dryad is not going to be suitable.

On Mon, Apr 4, 2016 at 10:07 PM, Rafal Wiewiora notifications@github.com wrote:

I see - well I just thought it strange for our lab to be restricting a dataset - why not have it available pre-publication?

— You are receiving this because you were mentioned. Reply to this email directly or view it on GitHub https://github.com/choderalab/ensembler/issues/69#issuecomment-205599068