On Wed, Nov 30, 2011 at 10:30 AM, Peter Rice <[email protected]> wrote: > On 11/29/2011 07:09 PM, Fields, Christopher J wrote: >> >> On Nov 29, 2011, at 12:35 PM, Peter Cock wrote: >>> >>> Doesn't BioPerl just use the Staden libraries for this internally? >> >> Yes, and it uses an old version as well (via bioperl-ext). Much of this >> effort was to go into the biolib initiative for creating cross-lang bindings >> using swig, but that seems to be silent at the moment. I'm surprised Python >> doesn't have io_lib bindings. > > BioLib is just swig wrappers around the existing Bio* interfaces and > code, so it will not help in this case if the projects are too divergent. > > Could we set up a Bio* collection of data formats with examples and > note which projects can handle each one? > > We do not need any one project to cover everything - we can reasonably > expect users to use some other project to interconvert formats if there are > gaps. > > regards, > > Peter Rice > EMBOSS Team
Good plan. I suggest we make a repository on github, perhaps bio-data or something like that, under the recently created OBF account, https://github.com/OBF Peter R - do you have a GitHub account yet? If so we (me, Chris Field, etc) can give you access to the OBF org account. For licensing, where we are free to choose the licence, I would like to go with something as liberal as possible to allow the files to be used by any OSS project (or closed source project), (e.g. Public Domain, CC0, MIT/BSD) rather than something more principled but restricted like CC-BY or CC-BY-ND. However, as we know from recent Debian packaging discussion about test cases taken from UniProt, licensing and copyright of samples from a database is complicated. Here we must at least keep careful records about where data came from. Peter _______________________________________________ EMBOSS mailing list [email protected] http://lists.open-bio.org/mailman/listinfo/emboss
