[Bioperl-l] Project: BioPerl 2.0 (and beyond)

lin yu joycelin12 at gmail.com
Thu Apr 8 12:53:20 EDT 2010

Hi all

Thanks for the comments. I would try the project in R and python instead.
Thank you.

On Thu, Apr 8, 2010 at 9:34 AM, Chris Fields <cjfields at illinois.edu> wrote:

> On Apr 8, 2010, at 11:24 AM, Robert Bradbury wrote:
> > On 4/6/10, lin yu <joycelin12 at gmail.com> wrote:
> >> 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.
> >
> > Joyce, it isn't clear what you are really asking for here.  I did some
> > digging and it appears as if "R" is a statistical language derived
> > from S:
> > http://www.r-project.org/
> > It isn't clear whether there is currently a toolset of phylogenetics
> > applications that use R (if so could you provide a pointer or some
> > examples)?
> Answering for her, but there are many.  Here's one just via a Google search
> using 'R phylogenetics':
> http://www.r-phylo.org/wiki/Main_Page
> > In theory one can interface perl programs to anything since it has
> > complete system call capabilities.  Presumably the advantage from a
> > BioPerl standpoint is to have BioPerl deal with the databases, genes,
> > genomes, etc. (something R presumably does not do) and have R deal
> > with the statistics side of any analysis.  But one needs a more
> > complete examination of what statistical aspects of phylogenetics
> > BioPerl does not currently handle (and could be better handled by
> > taking advantage of features which R might have).
> >
> > [In my opinion currently there is already way too much overlap in
> > tools packages with BioPerl, BioPython and BioRuby -- and there is no
> > matrix regarding the capabilities or lack thereof with each of these
> > so one could easily tell which of the three could or should best be
> > interfaced to R.]
> Python has a very nice R interface I believe.
> > It looks as if the phyloinformatics project is here:
> >
> https://www.nescent.org/wg/phyloinformatics/index.php?title=Phyloinformatics_Summer_of_Code_2010
> > but it isn't clear whether there is any coordination between the
> > BioPerl side of things and the Phyloinformatics side of things.
> There is overlap between the two organizations to a certain extent.  I
> could see having a direct set of bindings to R would be very nice from the
> BioPerl standpoint, but the project is really more a general Perl project in
> this case (R isn't just about microarrays or biostats).  The lone Perl-based
> interface, RSPerl, is no longer maintained that I know of (I never got it to
> work).
> chris

Best regards
Joyce Lin

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