Comments on: “bioinformatic perl or python”

By: Bioinformatics » Blog Archives » Peroxisome Proliferator-Activated Receptors Animation

Tue, 25 Sep 2007 16:32:30 +0000

[...] “bioinformatic perl or python” I decided to create a new series of posts (a category to be more precise) that deals with some searches that reach the blog. I use a pretty nice logging application so it is easy to randomly select a Google search term to discuss about it. About an… [...]

By: Acer

Acer — Sun, 16 Sep 2007 08:47:23 +0000

Java is fine in its limited place but it isn’t a scripting language like Python/Perl which is why the latter are preferred for much bioinformatics research. Python and Perl are also robust and cross platform. Just because you like Java doesn’t mean it is better suited for bioinformatics.

By: Bioinformatics » Blog Archive » JOBS - Bioinformatics Ph.D. student position

Sat, 15 Sep 2007 21:06:46 +0000

[...] About an hour ago someone in the interwebs searched for “bioinformatic perl or python” and my other blog is the third returned by Google. How can answer this question without praising too much Python or not despising too much perl? … …more [...]

By: Jon Harrop

Jon Harrop — Sat, 15 Sep 2007 16:10:28 +0000

Have you considered OCaml or F#?

By: Dean

Dean — Sat, 15 Sep 2007 13:50:48 +0000

Java should be used. It’s robust, cross platform, and fast. Just because you didn’t like it doesn’t mean it’s unsuitable for bioinformatics.

By: Mark

Mark — Sat, 15 Sep 2007 07:36:50 +0000

R is quite a different beast than Perl/Python and is really much more complementary in its capabilities to them. Indeed, R has some good interfaces with both Perl and Python. The combination can be quite a comprehensive computational tool set.

Personally I find that Python’s semantics is an acquired taste which will likely continue to restrict it’s popularity. On the other hand Perl’s concise and often cryptic syntax was never originally intended for writing anything but relatively short scripts. The recently popularity of the Ruby language has sort of stolen the spotlight from both of these scripting languages. Both Perl and Python are currently struggling with upcoming new and incompatible language releases (particularly Perl …).

By: Prock

Prock — Sat, 15 Sep 2007 03:12:27 +0000

perl has interactive shell: perl -de0

By: tim

tim — Thu, 13 Sep 2007 14:45:52 +0000

Ahhh, now I re-read the first paragraph, it makes a lot more sense… Heh, personally, I use R and Java for the majority of my work…(but I hope you don’t hold that against me)

By: nuin

nuin — Thu, 13 Sep 2007 14:19:04 +0000

Allan: the reason my “conclusion” was a tie it is because languages are a matter of personal taste. Tcl/Tk can be used with Python too, but wxPerl is not as a good as wxPython, that’s why I gave an advantage to Python there. But it is marginal and everything depends on the base language you are using, your personal taste (again) and the target of your application.
The whitespace management is, again, a personal taste. Some people love it, others hate it.

Tim: R is a great option and bioconductor is an excellent project. Those are two top environments to work with, specially in science and bioinformatics. Great tip. I did not mention anything about other languages in my post, just because it was started as an answer to the search.

Paulo

By: tim

tim — Thu, 13 Sep 2007 13:21:21 +0000

btw: I’m not trying to force another language on you, just pointing out other popular options to look into