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comp.lang.ruby

what could be improved in Ruby for Science?

Diego Virasoro

5/13/2009 1:34:00 PM

Hello,
I've noticed that languages such as Python are becoming more and more
fashionable with the Scientific communities, along side more hard core
classics like Fortran and Java.

Do you think Ruby is missing some piece of technology to be useful in
science? Or poor libraries?
In the end what do you think that could be done to make Ruby more used
in Science?

Diego
18 Answers

Phlip

5/13/2009 2:02:00 PM

0

Diego Virasoro wrote:

> I've noticed that languages such as Python are becoming more and more
> fashionable with the Scientific communities, along side more hard core
> classics like Fortran and Java.

Bioinformatics requires repeatedly shoveling huge blobs of data thru simple &
not necessarily fast filters. Python (and Perl) scored early adoption here. They
have nothing, technically, that Ruby doesn't have, including the slow part.

> Do you think Ruby is missing some piece of technology to be useful in
> science? Or poor libraries?
> In the end what do you think that could be done to make Ruby more used
> in Science?

All Ruby needs is better libraries, supporting an interacting community of
practitioners. Everyone needs faster a Ruby, and we have all the same
visualization tools as Python.

--
Phlip

cnjohnson

5/13/2009 2:39:00 PM

0


On May 13, 2009, at 8:35 AM, Diego Virasoro wrote:

> Hello,
> I've noticed that languages such as Python are becoming more and more
> fashionable with the Scientific communities, along side more hard core
> classics like Fortran and Java.
>
> Diego
>
With the advent of ruby 1.9.1, the only advantage here at ACCRE of
fortran, c and c++ is speed. The multi-threaded, multi-processor,
multi-node jobs that we see could just as easily be done in ruby with
the appropriate library support. However, the fortran libs that do
FFT, say, have been honed over the last 40 years to provide speeds
only slightly slower than code done in assembler. Ruby, java, python
simply do not offer that. That does not mean that ruby could not be
used to *drive* such code. As more and more people in our science
departments discover the advantages of using ruby to access pre-built,
pre-optimized libs the move to using ruby will continue.

Cheers--

Charles
---
Charles Johnson
Advanced Computing Center for Research and Education
Vanderbilt University

Greg Donald

5/13/2009 2:51:00 PM

0

On Wed, May 13, 2009 at 8:35 AM, Diego Virasoro
<Diego.Virasoro@gmail.com> wrote:
> Hello,
> I've noticed that languages such as Python are becoming more and more
> fashionable with the Scientific communities, along side more hard core
> classics like Fortran and Java.
>
> Do you think =A0Ruby is missing some piece of technology to be useful in
> science? Or poor libraries?
> In the end what do you think that could be done to make Ruby more used
> in Science?

Sounds like personal choice to me.

But for example Matt Wood stated he processes 250TBs of genetics data
per day with Ruby:

http://www.vimeo.com/1104164?pg=3Dembed&sec...

I'm working in genetics research as well, and we're really only using
Rails for our new web dev projects.


--=20
Greg Donald
http://des...

Phlip

5/13/2009 3:22:00 PM

0

Charles Johnson wrote:

> With the advent of ruby 1.9.1, the only advantage here at ACCRE of
> fortran, c and c++ is speed. The multi-threaded, multi-processor,
> multi-node jobs that we see could just as easily be done in ruby with
> the appropriate library support. However, the fortran libs that do
> FFT, say, have been honed over the last 40 years to provide speeds
> only slightly slower than code done in assembler. Ruby, java, python
> simply do not offer that. That does not mean that ruby could not be
> used to *drive* such code. As more and more people in our science
> departments discover the advantages of using ruby to access pre-built,
> pre-optimized libs the move to using ruby will continue.

That is exactly how videogames work. The lowest layer is custom display
hardware. Above that are drivers that manage huge strings of raw
instructions.

Above that is tuned C++ to manipulate the huge strings. And above that is a
soft scripting language - typically Lua - to assemble the C++ primitives
into programmable actors who interact in scenarios.

When something is slow, you move it down one layer in the stack. So most new
programming should happen in Lua, per the rule "premature optimization is
the root of all evil".

--
Phlip


Joshua Ballanco

5/13/2009 7:53:00 PM

0

On May 13, 2009, at 9:35 AM, Diego Virasoro wrote:

> Hello,
> I've noticed that languages such as Python are becoming more and more
> fashionable with the Scientific communities, along side more hard core
> classics like Fortran and Java.
>
> Do you think Ruby is missing some piece of technology to be useful in
> science? Or poor libraries?
> In the end what do you think that could be done to make Ruby more used
> in Science?

I have a sneaky suspicion that Ruby is being much more widely used in
Science than you might guess based just on forum posts and Google
searches. I think the biggest difference between science in Python and
science in Ruby is the sharing. For example, I'm using Ruby for some
evolutionary modeling for my Ph.D. thesis. I've thought about library-
izing some of the code, but that's extra effort. In other words, it
seems like Ruby is almost "too good" in that it lets you do really
rapid development of experimental code without the need to first write
entire libraries. The first step in building a better science-ruby
community is remembering to share.

In that respect, let me be the first to post a link to http://sciruby.codeforp...
, although it seems to be down (paging Dr. Howard?). Now, there's
another problem in that, as has been mentioned, Python and Perl are
technically no better than Ruby for this sort of work. Of course, the
flip side of that is that Ruby is no better than they are, and they
already have communities with critical mass. So, maybe what Ruby
really needs is to be *better* than Perl and Python.

On that topic, one idea I've been batting around in my head is
extending Ruby's prototyping capabilities and making Ruby methods
first class objects. This would have to either be a Ruby 2.0/2.1 goal,
or a fork of Ruby proper. However, what I imagine is that adding these
two pieces would make Ruby simply unbeatable for all classes of Object
composition patterns of programming (not just scientific programming).

...in my head there's also a graphical representation of Ruby objects
as blocks and methods as slots in the blocks with lots of wires making
logical connections and it's all equally code-able graphically and
textually...

Cheers,

Josh

-lim-

5/13/2009 8:34:00 PM

0

> So, maybe what Ruby =A0
> really needs is to be *better* than Perl and Python.

I'd rather say it needs to be better than a specialized programming
language like R or whatever other language/environment is generally
preferred in your domain of expertise.

Steven Hong

5/13/2009 11:45:00 PM

0

[Note: parts of this message were removed to make it a legal post.]

Hi all,

Steven with Manning Publications here. I wanted to let you know that
we've recently published two books on Ruby:

The Well-Grounded Rubyist by David A. Black
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with the same sharp focus and clear writing that made the first book
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Ruby in Practice by Jeremy McAnally and Assaf Arkin
For those already familiar with Ruby, Ruby in Practice will take your
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in a clear problem/solution format.

Until Friday, May 22, you can get either or both books for 40% off at
manning.com with the code "rubytalk40".

Steven Hong
Marketing Coordinator
Manning Publications
www.manning.com
===================
Skype: stevenhong02
Twitter: ManningBooks

Joel VanderWerf

5/13/2009 11:50:00 PM

0

Steven Hong wrote:
> Hi all,
>
> Steven with Manning Publications here. I wanted to let you know that
> we've recently published two books on Ruby:

Thread-hijacking + marketing is not a good mix.

--
vjoel : Joel VanderWerf : path berkeley edu : 510 665 3407

jzakiya

5/14/2009 12:45:00 AM

0

On May 13, 6:50 pm, Joel VanderWerf <vj...@path.berkeley.edu> wrote:
> Steven Hong wrote:
> > Hi all,
>
> > Steven with Manning Publications here. I wanted to let you know that
> > we've recently published two books on Ruby:
>
> Thread-hijacking + marketing is not a good mix.
>
> --
>        vjoel : Joel VanderWerf : path berkeley edu : 510 665 3407

Have a look at the Maya Project (ruby in astrophysics).

http://www.artcompsci.org/kali/five-year-...

Robert Dober

5/16/2009 12:26:00 PM

0

On Wed, May 13, 2009 at 9:52 PM, Joshua Ballanco <jballanc@gmail.com> wrote=
:
> On May 13, 2009, at 9:35 AM, Diego Virasoro wrote:
>
>> Hello,
>> I've noticed that languages such as Python are becoming more and more
>> fashionable with the Scientific communities, along side more hard core
>> classics like Fortran and Java.
>>
>> Do you think =A0Ruby is missing some piece of technology to be useful in
>> science? Or poor libraries?
>> In the end what do you think that could be done to make Ruby more used
>> in Science?
>
> I have a sneaky suspicion that Ruby is being much more widely used in
> Science than you might guess based just on forum posts and Google searche=
s.
> I think the biggest difference between science in Python and science in R=
uby
> is the sharing. For example, I'm using Ruby for some evolutionary modelin=
g
> for my Ph.D. thesis. I've thought about library-izing some of the code, b=
ut
> that's extra effort. In other words, it seems like Ruby is almost "too go=
od"
> in that it lets you do really rapid development of experimental code with=
out
> the need to first write entire libraries. The first step in building a
> better science-ruby community is remembering to share.
>
> In that respect, let me be the first to post a link to
> http://sciruby.codeforp..., although it seems to be down (paging D=
r.
> Howard?). Now, there's another problem in that, as has been mentioned,
> Python and Perl are technically no better than Ruby for this sort of work=