[BioRuby] Bringing the fun back to programming! (The first BioRuby IRC conference on Dec 19th)

[Francesco Strozzi]

Hi Piotr,
It's been a while since I started collaborating with Jan Aerts to develop
the Ruby Ensembl API. It was a good chance for me to learn Ruby and develop
bioinformatics programs. But I have to admit that, as you said, Ruby isn't
so powerful for bioinformatics compared to other languages. So, like you, I
feel the need to add another language for "real" and "though" bioinformatics
work and I have started learning Python in the last months which it's really
impressive. The core library is very poweful and BioPython is updated every
3 months (so it is under constant development). The performance of many
common tasks (e.g. parsing a large Blast report) are superior than with
BioRuby libraries, for what I have seen. But Ruby syntax and logic is simply
amazing (and to me even better than Python) and it's a shame we don't have
powerful solutions to bring Ruby out of the "just for the web" corner where
it was put since Rails outbreak. So, from my point of view, every effort
that could make Ruby shine for bioinformatics...well, is really really
appreciated and I want to hear and read more!
>From the technical point of view I have a couple of (newbie) questions:
 - I have no idea what Clojure and Scala are, so a sort of "Functional
Programming for Dummies" will be appreciated.
 - How much Java one need to know in order to be productive with
Ruby/BioRuby and Java/BioJava using JRuby?
   Because from my point of view, a Ruby programmer I think doesn't really
want to learn Java (which is a big language but with it's own issues and is
not so flexible as Ruby or Python).

So in the end, I will read and hear with interest what you can tell us about
your experience and future directions for Ruby/BioRuby development.

Cheers
Francesco


On Sat, Dec 11, 2010 at 10:46, Pjotr Prins <pjotr.public14 at thebird.nl>wrote:

> Hi Rubyistas,
>
> We have a special community, with a special language. Ruby is one of
> the most fun languages to work with, and we know it.
>
> Here I want to argue that for bioinformatics JRuby is one of the most
> exciting developments. Not only is it pretty fast, once compiled,
> but it also allows easy integration with Java (and BioJava). Before
> you recoil in horror, it also allows integration with some really cool
> programming languages, i.e. Scala, Clojure and Groovy.
>
> You know Ruby is great. But it has some weaknesses too. For
> Bioinformatics (B) and big data (BD) the problems are:
>
> (1) Weak B functionality
> (2) BD performance issues
> (3) So so parallel computing support (for BD)
> (4) Only partial functional programming support
>
> (1) and (2) can be resolved by using JRuby, BioJava and the JVM. (3)
> and (4) can be resolved by tapping into Scala and Clojure.
>
> Let me try to explain.
>
> (1) Weak B functionality: BioRuby is a great achievement, but I have a
> number of criticisms. First is that it is not suitable for BD. Almost
> every module loads all data in RAM, and there is no concept of
> parallel computations in the design. Finally the development is not
> fast - we are suffering from the fact that we are a small community.
> You could argue about reasons, but I don't think we should spend
> energy on the past, when there is such an obvious way forward. Let me
> continue.
>
> (2) BD performance issues: Ruby is slow. By definition compared to
> statically typed and compiled languages (such as C, Java, Scala,
> Clojure). It is pretty amazing to see how much speed Ruby 1.9 has.
> But, for BD it breaks down quickly. Ruby's strength is in beauty of
> code, but not in raw power.
>
> (3) So so parallel computing support (for BD): Functional languages
> (Haskell, Erlang, Scala, Clojure) have immutable data, and
> abstractions for parallelization, such as shared memory and actors,
> which make it much easier to write parallelized code. For performance
> and BD, this is extremely useful.
>
> (4) Only partial functional programming support: Once you get into
> functional programming you realize Ruby gets in the way. Support for
> functional programming in Ruby is patchy, though there is some.
>
> It is no accident that I have started the BioScala project, and Jan Aerts
> has
> started the BioClojure project in 2010 (!) BioRuby has spin-offs.
>
> My experience with Scala has been great. Scala is statically typed,
> and very fast. It also allows beautiful code with functional
> programming and parallelization thrown in. For me, there is a clear
> path where I use Ruby and Scala on a 50/50 basis. Essentially using
> the best of both worlds. JRuby is key to combining them.
>
> And, you know what? It is great fun!! I would get frustrated if I was
> locked in either language. But now it is seamless moving between the
> two, thanks to the JVM. Which, btw, these days can outperform even C
> code.
>
> Believe me, even two years ago, I would not have thought I would
> *ever* champion the JVM. But as a saaientist, you go by evidence.
>
> Programming is fun. And it has not ever been this great. I want to
> share that with you, and I would like to use the coming holiday
> season, and years after, to pass that on. I would guess Jan thinks the
> same way about Ruby and Clojure.
>
> Who is interested in getting back into the fun of programming? Who
> wants to experiment and become an even more productive programmer?
> It could be the goal of BioRuby in 2011 to show the way to other Bio*
> projects of handling development in such a way that we can easily move
> between the strengths of dynamic programming languages and high
> performant functional languages.
>
> I would like that.
>
> Pj.
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