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Question: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
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gravatar for Deanne Taylor
10.6 years ago by
Deanne Taylor50 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 -- --- 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
affylmgui limmagui • 649 views
ADD COMMENTlink modified 10.5 years ago by ilhami visne10 • written 10.6 years ago by Deanne Taylor50
Answer: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
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gravatar for Scott Markel
10.6 years ago by
Scott Markel50
Canada
Scott Markel50 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 San Diego, CA 92121 fax: +1 858 799 5222 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
ADD COMMENTlink written 10.6 years ago by Scott Markel50
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 > San Diego, CA 92121 fax: +1 858 799 5222 > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > -- Paul Geeleher Department of Mathematics National University of Ireland Galway Ireland
ADD REPLYlink written 10.6 years ago by Paul Geeleher1.3k
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... Best, Oleg 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 >> San Diego, CA 92121 fax: +1 858 799 5222 >> 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 >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor at stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > -- Dr Oleg Sklyar * EBI-EMBL, Cambridge CB10 1SD, UK * +44-1223-494466
ADD REPLYlink written 10.6 years ago by Oleg Sklyar260
Answer: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
0
gravatar for Pierre-Yves
10.6 years ago by
Pierre-Yves120
Pierre-Yves120 wrote:
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! I have been pointed not long ago to http://genomebiology.com/2008/9/7/r118 If that can help. Regards, Pierre
ADD COMMENTlink written 10.6 years ago by Pierre-Yves120
Answer: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
0
gravatar for Hervé Pagès
10.5 years ago by
Hervé Pagès ♦♦ 13k
United States
Hervé Pagès ♦♦ 13k wrote:
Hi Deanne, Maybe not strictly speaking for non-command-line-using users but the "Inference for R" software (not free) allows Microsoft Office users to use R (and R packages) as a scripting language from within an Office document. The code and the data are embedded in the document so, in theory, sharing these documents between users should be easy: http://inferenceforr.com/ Don't miss the 2-minute overview screencast and try to not get to upset by their claim that R lacks facilities to perform reproducible reasearch. (BTW the use of GUIs in general is making reproducible reasearch harder.) Disclaimer: I didn't try "Inference for R" myself and have no plans to use this kind of product. H. 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 > >
ADD COMMENTlink written 10.5 years ago by Hervé Pagès ♦♦ 13k
Answer: Is anyone developing an extensible Galaxy-like interface for Bioconductor?
0
gravatar for ilhami visne
10.5 years ago by
ilhami visne10
ilhami visne10 wrote:
I work on a project, called RGG (R GUI Generator), http://rgg.r-forge.r-project.org . It is still in development phase. The very first idea behind RGG was making a GUI for R scripts, which we have written ourself. So the others, you know who, can make use of R. For describing the GUI, it uses XML. Such GUIs developed by the community will be hosted in a public repository. Any question? I'm pleased to answer all. cheers, ilhami
ADD COMMENTlink written 10.5 years ago by ilhami visne10
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