[BioRuby] BioRuby Digest, Vol 82, Issue 9

[Pjotr Prins]

Hi Carl,

On Sat, Jul 28, 2012 at 09:43:16PM -0400, Carl Crott wrote:
> I'm wondering if anyone has established a list of the requirements for
> additional bio-gems...

Not systematically. github issues, at this point, appear to list new
ideas.

> I was hoping to do some development work on a gem to integrate with KEGG /
> Genomeweb but it seems there is no central repo for the features which we'd
> like to see.  This might be something to keep track of in the github
> feature area...  I cant help but think that feature requests for gems will
> be lost in a mailing list like this over time.

For sure.

> Specifically MR. Goto and Mr. Barton I've talked to you both about
> programming some things ... however maybe something I should work on
> instead is pulling together a feature list of all the features for each
> bio-gem.  Without a doubt they'll change over time .. but I think something
> thats slightly more static and more searchable ( Gmail's partial-string
> search is surprisingly bad ) would be a good idea.
> 
> If you guys like this idea I'd be happy to work on it ... or any API
> related bio-gem which happens to have a list of required features.

That would be very interesting :) Have you seen?

  https://www.relishapp.com/cucumber/cucumber/docs/drb-server-integration

Basically it presents features in a nice way. I like cucumber
features, and together with issues we could use that to track feature
requests and new ideas. Like I did with

  https://github.com/pjotrp/bioruby-alignment/issues/2

You can see I gave it the label 'Newbie', it could have had a label
'Feature'. There is a link to the feature that describes it:

  https://github.com/pjotrp/bioruby-alignment/blob/master/features/edit/gblocks.feature

My proposal would be to track github biogem repositories for issues
and features. For those features that fit nowhere (such as your
KEGG/Genomeweb gem) we could create a new project

  http://github.com/bioruby/new_features

To tie this all together we need some scripting for a web page, which
could be listed on http://biogems.info/features.html.

I would certainly like that!

Also I am interested in your RSS scraper for peer reviewed journals.
It would be nice to have news items on
http://biogems.info/journals.html which would list papers that
somehow seem relevant to FOSS.

Pj.