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

Robert Buels rmb32 at cornell.edu
Wed Apr 7 19:47:59 EDT 2010

Note that one of the Perl Foundation project ideas is a a better way of 
calling R from Perl.


Peter wrote:
> 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)
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