[BioC] Is anyone developing an extensible Galaxy-like interface for Bioconductor?

Herve Pages hpages at fhcrc.org
Mon Aug 4 18:59:27 CEST 2008

Hi Deanne,

Maybe not strictly speaking for non-command-line-using users but the
"Inference for R" software (not free) allows Microsoft Office users to
use R (and R packages) as a scripting language from within an Office document.
The code and the data are embedded in the document so, in theory, sharing
these documents between users should be easy:


Don't miss the 2-minute overview screencast and try to not get to upset
by their claim that R lacks facilities to perform reproducible reasearch.
(BTW the use of GUIs in general is making reproducible reasearch harder.)

Disclaimer: I didn't try "Inference for R" myself and have no plans to use
this kind of product.


Deanne Taylor wrote:
> Dear all:
> Iis anyone aware of  any projects creating an extensible platform that can act as an interface to Bioconductor that could be used to deliver Bioconductor methods to non-command-line-using users?
>  To save some replies: 
> * I am aware of limmaGUI and affylmGUI, but the tcl/tk interface is frustrating to some users who have difficulty installing tcl/tk independently while having R recognize it.  Macs and some *nix have been particularly problematic for some reasons.
> * I am also aware of CARMAweb, bioconductor packages and a few other basic R-web-interfaces, but I would like something more extensible outside of the R framework that could work both in R and in Python/Perl for example. Something more modular.
> *  I'm thinking something like Galaxy or Bioclipse. I realize Ross Lazarus is working on Rgenetics against Galaxy and Galaxy might be a good solution.
> If anyone is aware of other projects (beginning or ongoing or planned) in this area, I'd deeply appreciate getting pointers to them!
> Deanne

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