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The SciRuby Manifesto
Ruby has no equivalent to the beautifully constructed numpy, scipy, and matplotlib libraries for Python. We believe that the time for a Ruby science and visualization package has come and gone. Sometimes when a solution of sugar and water becomes super-saturated, from it precipitates a pure, delicious, and diabetes-inducing crystal of sweetness, induced by no more than the tap of a finger. So it is, we believe, with the need for numeric and visualization libraries in Ruby.
We are not the first with this idea, but we want to bring it to life.
As a further note, we believe that Ruby scripts are no different from the methods used in a mechanical experiment (e.g., the wetlab), and must be published along with any ''published'' derivative experimental results. The license for SciRuby shall likely reflect this, ultimately.
We are Rubyists, lovers of chunky bacon, and scientists. Driven mad by the glee of our Python-loving colleagues, we came together humming Les Mis.
You should join us! Sign up by filling out this form.
Currently, we are:
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John T. Prince, Department of Chemistry & Biochemistry, Brigham Young University
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John O. Woods, Marcotte Lab, The University of Texas at Austin
First and least, Ruby is a language with a sense of humor.
But more importantly, numerical computation and visualization can be done much better in Ruby, for a number of reasons:
- ''Everything returns a value.'' Ruby's better object model means better of chaining of computation.
- ''Iterators'' are way better than ''for'' loops.
- ''Readability.'' Ruby is incredibly readable, which makes it uber-maintainable.
- ''Metaprogramming.'' Sometimes the simplest solution is to write a [http://github.com/wycats/thor code generator]. Sometimes, eigenclasses are the cleanest.
- ''Integration into Rails.'' The influence of Rails on Ruby is undeniable. Web-based visualization for scientific projects is the future.
- ''R is nice but clunky.'' The learning curve is enormous. It does some things very well, and others not very well at all.
- rsruby, rinruby, simpler: gems which connect Ruby to R
- flotomatic: Rails gem for the Flot Javascript library, for web data visualization.
- Ruby GSL: Ruby interface for the GNU Scientific Library
All published results obtained using our code must include online publication of any and all source code using our libraries. (This refers not to the constituent parts, but to SciRuby as a whole.)
Most of the tools necessary for SciRuby already exist. NArray handles numeric computation; Statsample is a statistical library; and Rubyvis is a Ruby interface for Protovis, for visualization.
We hope to tie these tools together -- imagine the One Ring, but made of Ruby rather than gold -- and improve them, by providing code, documentation, and a community.
The broad success of Python is due, in large part, to its numerical computing core, [http://numpy.scipy.org/ numpy]. A few examples: h5py, pymol, mdanalysis, etc.
Goals: Stable, robust, fast, extremely well-documented core numerical library.
NArray is a fantastic library that has served the community for many years, and it meets many of our requirements (below). Its author has stated a desire to include a rewrite in ruby-core, but notes that he is years away from completing the rewrite. We want to offer him support in that endeavor.