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

Chris Fields cjfields at illinois.edu
Wed Apr 7 21:00:13 EDT 2010

I think this fits a general Perl/Python/etc project more; R isn't only BioC.


On Apr 7, 2010, at 6:47 PM, Robert Buels wrote:

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