[BioRuby] bioruby vs bioX

Yannick Wurm yannick.wurm at unil.ch
Fri Jul 23 10:39:10 UTC 2010

Dear List,

Here's a thought for a rainy morning. 
Thanks to new technologies, many biologists end up with large amounts of data & need to figure out a way to script things.
They can be caricatured into a few categories:
	- many attempt PERL because it's the only language they (or their boss) have heard of
	- others attempt to use R because that's what they learned in their undergraduate biostatistics course
	- others yet figure out that Python or Ruby are modern alternatives to Perl.... but I think most end up using Python, mostly because they find many examples of biopython code online.

Thus most newcomers to bioruby are not newbie biologists but computer geeks that know that ruby is great & need to tackle something biological.
I think we're really missing out on the newbie "I'm a biologist & I need to script" market.

Yes, there are a few resources, Eg:
	- Jan's article: http://www.biomedcentral.com/1471-2105/10/221   (are you planning a followup where you show some of bioruby... say to parse blast results & retrieve the corresponding sequences from genbank)?
	- a few wonderful but still randomly scattered blog posts
 	- http://bioruby.open-bio.org/wiki/SampleCodes
	- http://bioruby.open-bio.org/wiki/Tutorial
	- and an almost pathetically empty http://bioruby.open-bio.org/wiki/HOWTOs

But only few of these are "biologist non-programmer newbie-proof". And there is no central place to point a complete newbie.

Contrast that with the amount of information and ***code that works right away even if you don't understand the details*** found:
	- in the Biopython cookbook (yes it's ugly, but it does contain example code for most newcomer's questions)
	- on the Scriptome Perl "illegible one-liners that people use":

It is clear that we have a lot of potential. I wonder if proposals for contributions (such as Emanuele's) could not be geared towards improving our newbie-accessibility? I don't like having to point people towards Python/Biopython instead of ruby/Bioruby.


          yannick . wurm @ unil . ch
Ant Genomics, Ecology & Evolution @ Lausanne

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