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

Jarno Tuimala jtuimala at csc.fi
Mon Aug 4 09:06:17 CEST 2008


We have developed, and continue to develop Chipster, a graphical user interphase 
build on top of R and Bioconductor. It is currently steered mostly towards DNA 
microarray data analysis, but it can be easily extended with any R function, 
Java code or command line tool.

Chipster is a client-server system, and it requires a *NIX backend for server 
components, but the client is platform independent. It is also possible to set 
up a stand-alone version of Chipster on a Linux machine. As such, it might be a 
little heavy-weight for your purpose.

Currently we have made binaries available in SourceForge, but we are planning on 
releasing the sources also, since the system is open source. Please see 
http://chipster.csc.fi/ for more information.

If you'd like to get a test license, you can contact us on chipster at csc.fi.


> Date: Fri, 01 Aug 2008 15:52:22 -0400
> From: "Deanne Taylor" <DTAYLOR at hsph.harvard.edu>
> Subject: [BioC] Is anyone developing an extensible Galaxy-like
>        interface       for     Bioconductor?
> To: <bioconductor at stat.math.ethz.ch>
> Message-ID: <48933135.2DE5.00B2.0 at hsph.harvard.edu>
> Content-Type: text/plain; charset=US-ASCII
> 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
> --
> ---
> Deanne Taylor PhD
> Department of Biostatistics
> Harvard School of Public Health
> 655 Huntington Avenue
> Boston, MA 02115
> Office: 617.432.2899
> Fax:    617.432.5619
> dtaylor at hsph.harvard.edu

Jarno Tuimala, PhD, bioinformatics, CSC, P.O.Box 405, FI-02101 Espoo, Finland
tel.: +358 9 457 2226, fax: +358 9 457 2302, e-mail: jarno.tuimala at csc.fi
CSC is the Finnish IT Center for Science, http://www.csc.fi/molbio

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