[BioRuby] bioruby tutorials

[Pjotr Prins]

On Thu, Mar 05, 2009 at 09:40:44AM +0000, Jan Aerts wrote:
> Apart from the fact that we could try and finish the sample code at
> http://bioruby.open-bio.org/wiki/SampleCodes (although congratulations to
> the authors of what's already there!), we can try to think of use cases that
> go beyond just one class and actually reflect the bigger picture of a
> bioinformatics analysis. Something like "How to find conserved non-coding
> regions in a genome" which would be using bioruby's BLAST parser,
> Bio::Feature and maybe other classes as well.

Today I fixed the Tutorial to run with rubydoctest. This is a good way
of making sure the examples still work. Not everything is in there
yet, but I'll continue that work.

I just had a look at github gists - they are interesting as you can
embed them as syntax coloured code in web documents - while they are
single files in a git directory. I.e. we can create 'live'
documentation that can also run as tests, or example, code. This has
good potential for material that lives in the git repository. One
example:

  http://gist.github.com/13874

See the 'embed' link in the top right corner.

Now we still need to decide on a way of doing it for BioRuby. Jan,
maybe you can have a discussion in Japan.

Personally I don't like wikis for documentation - though they can make
it easier for people to contribute. But I have seen some real wild
growth in other projects. That is a crucial point. Are we willing to
drop the wiki? Or will we keep a wiki presence and I'll have to find a way
to keep the docs in sync?

Maybe I am the only one who feels the need for a resolution.

Pj.