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

Paul Geeleher paulgeeleher at gmail.com
Sat Aug 2 17:05:41 CEST 2008

I'm currently developing a web based interface to Bioconductor for an
organization in Ireland as part of a Masters degree. I can give you
more details if you are interested.


On Fri, Aug 1, 2008 at 9:54 PM, Scott Markel <smarkel at accelrys.com> wrote:
> Deanne,
> SciTegic Enterprise Server and Pipeline Pilot offer an extensible
> client-server data retrieval, filtering, analysis, and reporting
> platform.  Pipeline Pilot comes with many toolkits called collections.
> The Gene Expression Collection's core functionality is built on top of
> BioConductor.  The R-Statistics collection can be easily extended to
> add any desired additional BioConductor functionality.  The Professional
> client has a drag and drop visual icon/data flow interface; the web
> client can be configured to create different client interfaces.
> http://accelrys.com/products/scitegic/component-collections/gene-expression.html
> Scott
> 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
> --
> Scott Markel, Ph.D.
> Principal Bioinformatics Architect  email:  smarkel at accelrys.com
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Paul Geeleher
Department of Mathematics
National University of Ireland

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