[BioRuby] A question for BioRuby newbies

Thu Feb 9 09:04:22 UTC 2012

Hi Mic, 

On 08/02/12 23.38, "Mic" <mictadlo at gmail.com> wrote:

> Hi all,
> It would be great if BioRuby/Ruby would have:
> * a good BAM/tabix/vcf support
About BAM: https://rubygems.org/gems/bio-samtools but any suggestion
contribute or idea is more than welcome

> * http://www.scipy.org/
> * a powerful chart library like http://matplotlib.sourceforge.net/
https://github.com/SciRuby/sciruby
The developers are very active and some of them are working in
bioinformatics, but they want to keep it separated from BioRuby because
SciRuby can be useful for other purposes other than bioinformatics.
There was a graphic library http://rubyvis.rubyforge.org/ (there was a GSoC
project bio-images) now called http://mbostock.github.com/d3/ and another
library which uses SVG is http://raphaeljs.com/

> * http://networkx.lanl.gov/
About network I don't know.

> 
> 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
>> 
>> _______________________________________________
>> BioRuby Project - http://www.bioruby.org/
>> BioRuby mailing list
>> BioRuby at lists.open-bio.org
>> http://lists.open-bio.org/mailman/listinfo/bioruby
>> 
>> 
> _______________________________________________
> BioRuby Project - http://www.bioruby.org/
> BioRuby mailing list
> BioRuby at lists.open-bio.org
> http://lists.open-bio.org/mailman/listinfo/bioruby