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

Pjotr Prins pjotr.public14 at thebird.nl
Mon Dec 13 11:42:38 UTC 2010

On Sun, Dec 12, 2010 at 08:43:15PM +0100, Francesco Strozzi wrote:
> 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). 

Main comment would be that Python is not much different from Ruby. It
is interpreted, dymamic, and does not have good support for parallel
programming, nor the speed required for big data (BD). Perl, Python
and Ruby are really in the same boat.

> The performance of many common tasks (e.g. parsing a large Blast
> report) are superior than with BioRuby libraries, for what I have
> seen. 

Here you have a good point. BioRuby is lagging behind BioPython,
BioPerl and BioJava.

My proposal is to use BioJava together with BioRuby. You can do
something similar with Jython (Python on the JVM), though I have the
impression Jython is not as active as JRuby, anymore. JRuby is
getting strong industry support, at this point.

> 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. 

I know people who would disagree with that last statement...

To me, Ruby is a way of thinking, which is reflected in Rails.

> 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.

There are plenty online resources. The main Scala book is great.

>  - How much Java one need to know in order to be productive with
> Ruby/BioRuby and Java/BioJava using JRuby?

Not Java per se. Mostly it is getting used to the JVM world and docs.

>    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).

I agree. I personally dislike the Java language.

After a project around 2001 I vowed not to touch it again. It is not a
hard language, but merely a pain. I liked any of the other Bio*
languages better.

> 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.

My suggestion would be to study a language more removed from Python,
Ruby and Perl.

I will try to make a screencast.


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