[BioC] Is anyone developing an extensible Galaxy-like interface for Bioconductor?
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.
> On Fri, Aug 1, 2008 at 9:54 PM, Scott Markel <smarkel at accelrys.com> wrote:
>> 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.
>> 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!
>> 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
>> San Diego, CA 92121 fax: +1 858 799 5222
>> USA web: http://www.accelrys.com
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Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
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