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

Peter biopython at maubp.freeserve.co.uk
Wed Apr 7 18:13:52 EDT 2010

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.

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)

Peter (@Biopython)

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