[BioRuby] A question for BioRuby newbies

[Mic]

Hi all,
It would be great if BioRuby/Ruby would have:
* a good BAM/tabix/vcf support
* a gff3 support which doesn't read the whole file in the memory see
http://biopython.org/wiki/GFF_Parsing#Limiting_to_features_of_interest
* http://www.scipy.org/
* a powerful chart library like http://matplotlib.sourceforge.net/
* http://networkx.lanl.gov/

Maybe Google Summer of Code 2012 could help.

On Thu, Feb 9, 2012 at 6:52 AM, Michael Barton <mail at michaelbarton.me.uk>wrote:

> I think this is a very good idea. More public engagement
> would be a boon to the BioRuby project. I would be happy to
> help new developers work on my Scaffolder gem. Here are two
> additional suggestions from me for increasing BioRuby
> participation.
>
> First suggestion:
>
> I think the bioruby home page could be made simpler. A very
> rough estimate shows 80 links on the front page:
>
> curl http://bioruby.open-bio.org/ | tidy -i -q | grep href | wc
>  -> 80 links
>
> Compare this with the Rails and Sinatra homepages:
>
> curl http://rubyonrails.org/ | tidy -i -q | grep href | wc
>  -> 47 links
>
> curl http://www.sinatrarb.com/ | tidy -i -q | grep href | wc
>  -> 20 links
>
> I think making the homepage simpler would be very
> beneficial. For instance I think the two most important
> links (Tutorial and Sample codes) pages should be given much
> greater prominence. These are the two pages which most
> beginners will want to get started with. Compare with the
> Sinatra page which has only six links on the front page
> pointing to the most significant parts of the project.
>
> I think the Tutorial and Sample codes pages could do with
> some love also. These pages do not match the visual layout
> of the bioruby home page, one is in a separate domain while
> the other is a wiki page. I think these pages deserve
> attention to make them simpler and more accessible. A common
> CSS theme also provides a unified front to the BioRuby
> project.
>
> Compare with the Sinatra intro and documentation pages:
>  * http://www.sinatrarb.com/intro
>  * http://www.sinatrarb.com/documentation
>
> My opinion is that the BioRuby website should head in this
> direction. I am not a web designer but I am happy to
> contribute effort to writing web copy and BioRuby recipes. I
> also think that bioruby should also have its own web address
> too.
>
> Second Suggestion:
>
> I think as BioRuby becomes more and more popular the code
> base will continue to increase in size. I think this will
> become a disadvantage as a larger code base is harder to
> navigate, harder to maintain, and more intimidating to make
> contributions to.
>
> Pjotr has addressed this with the BioGems project but I
> think we should follow the natural progression and consider
> splitting the Bio gem into smaller self-contained gems. I
> think this is already starting to happen with the
> replacement gff3 and 'faster' fasta gems.
>
> I think smaller gems would be easier to maintain and allow
> different development cycles. I think it also easier to
> create a gem for a new idea rather than find a place for it
> in a large pre-existing code base. Finally this would follow
> the smaller 'does just one thing' gem development philosophy
> in Ruby.
>
> Michael Barton
>
> On Wed, Feb 08, 2012 at 07:48:17PM +0100, Pjotr Prins wrote:
>
> > Hi All,
> >
> > This mailing list counts 180 subscribed readers.
> > Which is impressive. Also since the introduction of
> > http://biogems.info/ the number of BioRuby downloads has
> > increased rapidly.
> >
> > You may also have noticed Ruby, in general, is making
> > its mark in bioinformatics. More and more people are
> > programming in Ruby, which I think rather delightful.
> > And Biogems.info is proving to be cutting edge, and
> > accelerating development.
> >
> > So here is a question to people who read the mailing list,
> > but do not necessarily participate. What is needed to pull
> > you in?
> >
> > At this point I have two ideas to increase participation.
> >
> > (1) First a race. I would like all readers to vote a few
> > times a year on the most beautiful Biogem source code.
> > We'll put up a few projects to choose from, and the winner
> > will be highlighted on http://biogems.info/. Ruby is about
> > beauty, and we are seeing some of that in the biogems.
> >
> > The other idea I got at FOSDEM this year from a convincing
> > talk by Brian Ostergard, titled 'You are doing it all
> > wrong'
> >
> >   http://fosdem.org/2012/schedule/event/really_grow_commun
> >   ity
> >
> > where he made a strong case to address inexperienced
> > developers. And you know what, I believe he is right. So
> >
> > (2) We will look for ways to get inexperienced developers
> > involved. One way is to define uncomplicated and
> > moderately complicated tasks, feature requests and bug
> > fixes.
> >
> > We are going to list these 'jobs' on http://biogems.info/.
> > If anyone picks up a task he/she will get very *strong*
> > support from the plugin owner, as well as the Biogem
> > maintainers. You, the programmer, will get all the credit
> > for the work.
> >
> > How does this sound? Does this appeal to you? Anyone of
> > the less experienced, or even experienced, wants to voice
> > his or her opinion? We may even turn some work into a
> > Google Summer of Code project proposal.
> >
> > Pj. _______________________________________________
> > BioRuby Project - http://www.bioruby.org/
> > BioRuby mailing list BioRuby at lists.open-bio.org
> > http://lists.open-bio.org/mailman/listinfo/bioruby
>
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>
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