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

Oleg Sklyar osklyar at ebi.ac.uk
Sun Aug 3 16:16:41 CEST 2008

Before you invest too much time yourself, have a look at BioCep, which 
is essentially a web-based interface to R, Bioconductor and much much 
more. http://biocep-distrib.r-forge.r-project.org/ I have no idea in 
which state is BioCep at the moment, but I have seen it working...


Paul Geeleher wrote:
> 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.
> -Paul.
> 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
>> Accelrys (SciTegic R&D)             mobile: +1 858 205 3653
>> 10188 Telesis Court, Suite 100      voice:  +1 858 799 5603
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>> USA                                 web:    http://www.accelrys.com
>> http://www.linkedin.com/in/smarkel
>> Board of Directors: International Society for Computational Biology
>> Co-chair: ISCB Publications Committee
>> Associate Editor: PLoS Computational Biology
>> Editorial Board: Briefings in Bioinformatics
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Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466

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