How do you use Ruby on Rails for science (if applicable)?

Question

We do research in systems biology. We prefer to use existing data sets, because collecting new biological data is expensive. Thus, a lot of the scripts we write are little more than transformations of one data set into another.

Eventually, we put our results online -- and more and more journals are requiring this sort of thing.

So it was no great leap for me to try using Rails for my projects. I can set up easily reproducible experiments, transform data step by step through database tables (e.g. using rake), and display results using gems like flotomatic and the gnuplot. If I need something to run very quickly, I can even write a custom gem in C++ using Rice, or parallelize using starling and workling.

Eventually, I started to wonder if anyone else was using Rails to do bioinformatics or science in general.

I thought, "If I were a science research Rails gem, what would I do?"

What extra features would such a gem have? Perhaps a Migration adaptation into a rake-able pipeline? Maybe more advanced graphing features? Built-in background jobs?

@Jasper: I don't have the reputation to edit a community wiki, but I'd like to participate. — Translunar
– Translunar, Commented Aug 26, 2010 at 16:55
It wasn't as much a question to you as it was a question to whoever was passing by with enough rep to make your post a community wiki (and if I 'm not mistaken, you can edit a community wiki if you were the original poster). The idea is that you don't get reputation for it, and it is usually applied to question that don't have a single answer (or which will have a different answer for each user as in your case or question which are clearly subjective) — Jasper
– Jasper, Commented Aug 26, 2010 at 19:09

Pierre · Accepted Answer · 2010-08-27 16:04:27Z

4

For Bioinformatics, see http://bioruby.org

answered Aug 27, 2010 at 16:04

Pierre

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Translunar Over a year ago

I am aware of bioruby, but this question is really about Rails.

Chmille4 · Accepted Answer · 2010-09-12 13:19:00Z

I agree with Pierre. I think bioruby is the right place. Many (most?) bioruby users/developers use rails, making rails a natural extension to the bioruby project.

Here's an incomplete list of bioruby code for rails:

Run bioruby console in a rail app - http://bioruby.open-bio.org/wiki/BioRubyOnRails
ActiveRecord (Rails default ORM) classes for Ensembl - bioruby-annex.rubyforge.org/
Plugin for Uniprot db - bioruby.g.hatena.ne.jp/nakao_mitsuteru/20070410/uniprot_on_active_record_plugin
CHADO/Bioruby integration effort - github.com/robsyme/RubyCHADO

sorry about the messed up links, but as a new user I can't post more than a single link :(

Ron Gejman · Accepted Answer · 2011-02-03 05:39:12Z

3

I've used Michael Barton's organized_experiments before. It works quite nicely once you replace DataMapper with ActiveRecord.

answered Feb 3, 2011 at 5:39

Ron Gejman

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Michael Barton Over a year ago

Ha! Fair enough. At the time DataMapper seemed like the new hotness so it was an excuse to give it a whirl. I retrospect AR was always going to be more supported and stable.

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