Question: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
9.0 years ago by
Jarno Tuimala • 140
Jarno Tuimala • 140 wrote:
Hello! 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. Jarno > 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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