[Bioperl-l] Project: R and Perl GSoC, was: BioPerl 2.0 (and beyond)

[Peter]

On Wed, Apr 7, 2010 at 2:18 AM, lin yu <joycelin12 at gmail.com> wrote:
> Hi
>
> I am from a part-time student from NUS. May i suggest the following project:
> Accessing R phylogenetic tools from BioPerl Actually this project was
> initially proposed by the Phyloinformatics Summer of Code 2010, however the
> programming language is in Python and I have no prior experience in that
> language. Therefore, I would like to propose the use of BioPerl in access R
> phlyogenetic tools or the combination of R and BioPerl in other similar
> applications like microarray analysis etc. Would it be possible? I would
> like to know the answer as soon as possible as I can edit my proposal in the
> case. Thank you.
> --
> Best regards
> Joyce Lin

Hi Joyce,

You said you don't have any Python experience, but your proposed
project would require you to know BOTH Perl and R (and R isn't that
easy to learn in my opinion).

The Python project you refer to would build on rpy2, a library for calling
R from Python. The aim was to target Biologically interesting things
supported in R, and make them usable from Python.
http://rpy.sourceforge.net/
http://biopython.org/wiki/Google_Summer_of_Code

For your project to be realistic, you would need to start with a way of
calling R from Perl (an interesting computer science project), and from
a quick Google there is the RSPerl project- but it hasn't been updated
for several years and I doubt it would work perfectly on recent versions
of R: http://www.omegahat.org/RSPerl/

Perhaps someone else on the list has some other suggestions? You
would also need someone to be a Google Summer of Code (GSoC)
mentor...

Peter (@Biopython)