[Open-bio-l] Common Sample Data Collection, was: SCF files (Staden)

[Pjotr Prins]

On Wed, Nov 30, 2011 at 10:41:37AM +0000, Peter Cock wrote:
> > 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.

It is a bit more than that. Mostly biolib is a multi-platform build system.

Code-wise, most libraries are not immediately suitable for wrapping
(SWIG of FFI), including EMBOSS, so adapters are required. I wrote an
example for EMBOSS/transeq, which outperforms all other Bio*
implementations (published in upcoming Springer book).

BioLib also does automated document generation (parsing SWIG XML) and
testing.

The current BioLib went into maintenance mode, after my visit to Chris
Fields. I see BioLib v1 as a proof-of-concept mostly, at this point,
though I use it, and I know of others. A new high performance library
is in the works - but these things move slowly.

> 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

Git is not very good for storing large data files, which we would want
to fetch partially. My suggestion would be to have a plain old file
repo, e.g. on S3, which can be mirrored by others.

Pj.