[Open-bio-l] a common repository for test datasets/use cases for all Bio* projects

[Peter]

On Thu, Dec 4, 2008 at 5:06 PM, Jason Stajich <jason at bioperl.org> wrote:
>
> I don't know if this is really the best email list for this -- although not
> sure what other common list should be used.

I think I suggested trying this list to Giovanni - it looked like the
best bet, although I suspect it has a fairly low subscriber count.

> We actually a started a project like this many moons ago, but no one
> contributed examples...
>
> http://code.open-bio.org/cgi/viewcvs.cgi/biodata/
>

That was before I started using Biopython, so I'd never seen that.

> We can start a common SVN repository for this if you like or a github on OBF
> if that is more likely to garner contributions.

Using an OBF repository would be nice, especially if developers from
all the Bio* projects with existing CVS/SVN accounts automatically had
write access to it.  I've not really used git, but it might be more
open for new-comers.

> In terms of documentation - you are certainly welcome to make a
> documentation repository but I would argue a wiki or wiki-like soln would be
> best for documentation.
> Whether a common wiki can be maintained among the projects (or merge the
> wikifarms someday) is something to contemplate too.

Given the OBF already has wiki software up and running, this does seem
like a good choice for documentation.

The BioPerl wiki already has a lot of useful stuff describing
different file formats, and in most cases the text is independent of
BioPerl.  It would make sense to take these pages as a basis for a
shared OBF wiki.  I would think that ideally the Bio* projects could
have a page on each file format describing how it is parsed with that
tool kit, but citing a shared file format description page (or even
embedding it on the fly).

Peter