Question: regarding web interface to R coding
0
gravatar for ankhee dutta
10.2 years ago by
ankhee dutta60
ankhee dutta60 wrote:
hi all, here i have done some coding in R and want a web interface which can execute the R coding after taking user's query (who don't have knowledge of R) in any format. Can you suggest some language or software made for this purpose and is used commonly. Any kind of help will be appreciable. -- Ankhee Dutta project trainee, JNU,New Delhi-67 [[alternative HTML version deleted]]
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ADD COMMENTlink modified 10.2 years ago by Steve Lianoglou12k • written 10.2 years ago by ankhee dutta60
Answer: regarding web interface to R coding
0
gravatar for Martin Morgan
10.2 years ago by
Martin Morgan ♦♦ 24k
United States
Martin Morgan ♦♦ 24k wrote:
ankhee dutta wrote: > hi all, > here i have done some coding in R and want a web interface which can execute > the R coding after taking user's query (who don't have knowledge of R) in > any format. Can you suggest some language or software made for this purpose > and is used commonly. RWebServices builds SOAP-based web services from R packages, with a separate 'service' front-end and 'worker' back end. See http://www.bioconductor.org/packages/bioc/html/RWebServices.html especially the 'Installing...' and 'Enabling... vignettes. > Any kind of help will be appreciable.
ADD COMMENTlink written 10.2 years ago by Martin Morgan ♦♦ 24k
Answer: regarding web interface to R coding
0
gravatar for Fraser Sim
10.2 years ago by
Fraser Sim270
Fraser Sim270 wrote:
You can also use ASP or ASP.NET languages to interface with R via statconn R (D)COM. http://sunsite.univie.ac.at/rcom/ Cheers, Fraser -----Original Message----- From: bioconductor-bounces@stat.math.ethz.ch [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ankhee dutta Sent: Monday, September 07, 2009 6:25 AM To: bioconductor at stat.math.ethz.ch Subject: [BioC] regarding web interface to R coding hi all, here i have done some coding in R and want a web interface which can execute the R coding after taking user's query (who don't have knowledge of R) in any format. Can you suggest some language or software made for this purpose and is used commonly. Any kind of help will be appreciable. -- Ankhee Dutta project trainee, JNU,New Delhi-67 [[alternative HTML version deleted]] _______________________________________________ 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
ADD COMMENTlink written 10.2 years ago by Fraser Sim270
Another possibility is Biocep-R, which is more Java-based than strictly web-based, although such distinctions are now blurring: http://biocep-distrib.r-forge.r-project.org/ I've not tried using it for anything serious yet, but it might fit your purposes if you want distributed access to a central R installation. Cheers, Tim 2009/9/7 Fraser Sim <fjsim at="" buffalo.edu="">: > You can also use ASP or ASP.NET languages to interface with R via statconn R > (D)COM. > > http://sunsite.univie.ac.at/rcom/ > > Cheers, > Fraser > > -----Original Message----- > From: bioconductor-bounces at stat.math.ethz.ch > [mailto:bioconductor-bounces at stat.math.ethz.ch] On Behalf Of ankhee dutta > Sent: Monday, September 07, 2009 6:25 AM > To: bioconductor at stat.math.ethz.ch > Subject: [BioC] regarding web interface to R coding > > hi all, > here i have done some coding in R and want a web interface which can execute > the R coding after taking user's query (who don't have knowledge of R) in > any format. Can you suggest some language or software made for this purpose > and is used commonly. > Any kind of help will be appreciable. > -- > Ankhee Dutta > project trainee, > JNU,New Delhi-67 > > ? ? ? ?[[alternative HTML version deleted]] > > _______________________________________________ > 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 > > _______________________________________________ > 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 >
ADD REPLYlink written 10.2 years ago by Tim Rayner270
Answer: regarding web interface to R coding
0
gravatar for Steve Lianoglou
10.2 years ago by
Denali
Steve Lianoglou12k wrote:
Hi Ankee, On Mon, Sep 7, 2009 at 6:24 AM, ankhee dutta<ankheedutta at="" gmail.com=""> wrote: > hi all, > here i have done some coding in R and want a web interface which can execute > the R coding after taking user's query (who don't have knowledge of R) in > any format. Can you suggest some language or software made for this purpose > and is used commonly. > Any kind of help will be appreciable. Here's a very timely blogpost from revolution computing: http://blog.revolution-computing.com/2009/09/interactive-stock- visualizations.html There are links to things like RApache and other libraries that helped with the construction of this R web application. Should be a good place to start. -steve -- Steve Lianoglou Graduate Student: Computational Systems Biology | Memorial Sloan-Kettering Cancer Center | Weill Medical College of Cornell University Contact Info: http://cbio.mskcc.org/~lianos/contact
ADD COMMENTlink written 10.2 years ago by Steve Lianoglou12k
Answer: regarding web interface to R coding
0
gravatar for Michael Dondrup
10.2 years ago by
Michael Dondrup140 wrote:
Hi Ankhee, depends mainly on your favorite host language I think. Among other suggestions (RPy), I think one of the most commonly used solution is Java and the rJava package. That can be installed from CRAN. That contains JRI so you can run R code from Java (and vice versa), I know some people that use rJava, and I do, it has little documentation but otherwise it works fine, and I think the Eclipse R plugin uses it too. Then you could build your web UI in Java using eg. JSF, Echo2, or ICEFaces. If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or try a patched version http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl where we have tried solve some issues. That worked for me at least on a variety of systems. But maybe noone else is using that. I don't like the "write script to temporary file and pass around tables in textfiles" approach too much, I thinks it's not a real clean and not very efficient approach. But that's only my 50cent ;) Michael Am 07.09.2009 um 12:24 schrieb ankhee dutta: > hi all, > here i have done some coding in R and want a web interface which can > execute > the R coding after taking user's query (who don't have knowledge of > R) in > any format. Can you suggest some language or software made for this > purpose > and is used commonly. > Any kind of help will be appreciable. > -- > Ankhee Dutta > project trainee, > JNU,New Delhi-67 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
ADD COMMENTlink written 10.2 years ago by Michael Dondrup140
Hello Michael, I agree the hack that I suggested is not the *Best Practice*, but it worked like a charm for me and I am using it in same way for several pipelines that requires R as a component for calculation alone - in such situations, I must say that its clean and extremely efficient. I thought of sharing it with Dutta, if he may need something like a quick hack, I spend several days to get my RSPerl up an running, but it didn't worked on my CentOS. But this one was as quick as writing a Perl script. Cheers, K. Shameer NCBS - TIFR > If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or > try a patched version > > http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl > where we have tried solve some issues. That worked for me at least on a > variety of systems. But maybe noone else is using that. > I don't like the "write script to temporary file and pass around tables in > textfiles" approach too much, I thinks it's not a real clean and not very > efficient approach. But that's only my 50cent ;) [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Shameer Khadar30
Thanks for replying Michael but sorry to say that i don't have much knowledge about java and its applications but you were also suggesting to use RSPerl, so will that solve my purpose of making web interface to the R coding, otherwise can i use CGIwithR package for the purpose, how is it and is this package common in use? Please do reply. On Mon, Sep 7, 2009 at 7:01 PM, Michael Dondrup <michael.dondrup@bccs.uib.no> wrote: > Hi Ankhee, > depends mainly on your favorite host language I think. Among other > suggestions (RPy), I think one of the most commonly used solution is > Java and the rJava package. That can be installed from CRAN. > > That contains JRI so you can run R code from Java (and vice versa), I know > some people that use rJava, and I do, it has little documentation but > otherwise it works fine, and I think the Eclipse R plugin uses it too. Then > you could build your web UI in Java using eg. JSF, Echo2, or ICEFaces. > > If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or > try a patched version > > http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl > where we have tried solve some issues. That worked for me at least on a > variety of systems. But maybe noone else is using that. > I don't like the "write script to temporary file and pass around tables in > textfiles" approach too much, I thinks it's not a real clean and not very > efficient approach. But that's only my 50cent ;) > > Michael > > Am 07.09.2009 um 12:24 schrieb ankhee dutta: > > hi all, >> here i have done some coding in R and want a web interface which can >> execute >> the R coding after taking user's query (who don't have knowledge of R) in >> any format. Can you suggest some language or software made for this >> purpose >> and is used commonly. >> Any kind of help will be appreciable. >> -- >> Ankhee Dutta >> project trainee, >> JNU,New Delhi-67 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > > > -- Ankhee Dutta project trainee, JNU,New Delhi-67 [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by ankhee dutta60
The choice of the appropriate language to build a user interface depends on - your skills in the programming languages - your requirements, e.g. full blown AJAX web 2.0 with virtual desktop in the browser behavior vs. single CGI page - availability of libraries for user-interfaces meeting these requirements I don't know about the first two points, maybe you should figure that out. but the UI doesn't come for free with any language solution and its construction might outweigh the implementing of the analysis. IMHO there are much better languages with support for building web- interfaces than R. The CGIwithR package could still work, but it has not been updated since 2005, I haven't tried it. Maybe the RApache package suggested by Steve is worth a try, too. If using a different prog. language you always need a sort of language binding such that you can call R functions in Perl, Python or Java (e.g. RSPerl, rJava, RPy, or transfer via tmpfiles, system commands), that doesn't give you the UI magically. Building small web-apps in Perl is quite straight forward though, for bigger ones I would (nowadays) try something else. Am 08.09.2009 um 06:21 schrieb ankhee dutta: > Thanks for replying Michael but sorry to say that i don't have much > knowledge about java and its applications but you were also > suggesting to > use RSPerl, so will that solve my purpose of making web interface to > the R > coding, otherwise can i use CGIwithR package for the purpose, how is > it and > is this package common in use? > Please do reply. > On Mon, Sep 7, 2009 at 7:01 PM, Michael Dondrup <michael.dondrup at="" bccs.uib.no="">> wrote: > >> Hi Ankhee, >> depends mainly on your favorite host language I think. Among other >> suggestions (RPy), I think one of the most commonly used solution is >> Java and the rJava package. That can be installed from CRAN. >> >> That contains JRI so you can run R code from Java (and vice versa), >> I know >> some people that use rJava, and I do, it has little documentation but >> otherwise it works fine, and I think the Eclipse R plugin uses it >> too. Then >> you could build your web UI in Java using eg. JSF, Echo2, or >> ICEFaces. >> >> If you like perl you might try RSPerl http://www.omegahat.org/ >> RSPerl/ or >> try a patched version >> >> http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl >> where we have tried solve some issues. That worked for me at least >> on a >> variety of systems. But maybe noone else is using that. >> I don't like the "write script to temporary file and pass around >> tables in >> textfiles" approach too much, I thinks it's not a real clean and >> not very >> efficient approach. But that's only my 50cent ;) >> >> Michael >> >> Am 07.09.2009 um 12:24 schrieb ankhee dutta: >> >> hi all, >>> here i have done some coding in R and want a web interface which can >>> execute >>> the R coding after taking user's query (who don't have knowledge >>> of R) in >>> any format. Can you suggest some language or software made for this >>> purpose >>> and is used commonly. >>> Any kind of help will be appreciable. >>> -- >>> Ankhee Dutta >>> project trainee, >>> JNU,New Delhi-67 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> >> >> > > > -- > Ankhee Dutta > project trainee, > JNU,New Delhi-67 > > [[alternative HTML version deleted]] > > _______________________________________________ > 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 Michael Dondrup, Ph.D. Bergen Center for Computational Science Computational Biology Unit Unifob AS - Thorm?hlensgate 55, N-5008 Bergen, Norway Phone: +47 55584029 Fax: +47 55584295
ADD REPLYlink written 10.2 years ago by Michael Dondrup140
On Tue, Sep 8, 2009 at 7:40 AM, Michael Dondrup <michael.dondrup@bccs.uib.no> wrote: > The choice of the appropriate language to build a user interface depends on > - your skills in the programming languages > - your requirements, e.g. full blown AJAX web 2.0 with virtual desktop in > the browser behavior vs. single CGI page > - availability of libraries for user-interfaces meeting these requirements > I don't know about the first two points, maybe you should figure that out. > but the UI doesn't come for free with any language solution and its > construction > might outweigh the implementing of the analysis. > I would echo these points and add that before doing such a task using R, it is probably worthwhile being pretty familiar with CGI/web applications, HTML, server-side versus client-side technologies, etc. This is probably best accomplished in perl/python only because the documentation/literature is rich. When you know about handling requests and generating responses, using R to do so or using a language binding to R can be less challenging, as the dynamics of web interaction can be quite challenging to grasp early on. > > IMHO there are much better languages with support for building > web-interfaces than R. The CGIwithR package could > still work, but it has not been updated since 2005, I haven't tried it. > Maybe the RApache package suggested by Steve is worth a try, too. > > If using a different prog. language you always need a sort of language > binding such that you can call R functions in Perl, Python or Java (e.g. > RSPerl, rJava, RPy, or transfer via tmpfiles, system commands), that doesn't > give you the UI magically. Building small web-apps in Perl is quite straight > forward though, for bigger ones I would (nowadays) try something else. > > Am 08.09.2009 um 06:21 schrieb ankhee dutta: > > > Thanks for replying Michael but sorry to say that i don't have much >> knowledge about java and its applications but you were also suggesting to >> use RSPerl, so will that solve my purpose of making web interface to the R >> coding, otherwise can i use CGIwithR package for the purpose, how is it >> and >> is this package common in use? >> Please do reply. >> On Mon, Sep 7, 2009 at 7:01 PM, Michael Dondrup < >> Michael.Dondrup@bccs.uib.no >> >>> wrote: >>> >> >> Hi Ankhee, >>> depends mainly on your favorite host language I think. Among other >>> suggestions (RPy), I think one of the most commonly used solution is >>> Java and the rJava package. That can be installed from CRAN. >>> >>> That contains JRI so you can run R code from Java (and vice versa), I >>> know >>> some people that use rJava, and I do, it has little documentation but >>> otherwise it works fine, and I think the Eclipse R plugin uses it too. >>> Then >>> you could build your web UI in Java using eg. JSF, Echo2, or ICEFaces. >>> >>> If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or >>> try a patched version >>> >>> >>> http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl >>> where we have tried solve some issues. That worked for me at least on a >>> variety of systems. But maybe noone else is using that. >>> I don't like the "write script to temporary file and pass around tables >>> in >>> textfiles" approach too much, I thinks it's not a real clean and not very >>> efficient approach. But that's only my 50cent ;) >>> >>> Michael >>> >>> Am 07.09.2009 um 12:24 schrieb ankhee dutta: >>> >>> hi all, >>> >>>> here i have done some coding in R and want a web interface which can >>>> execute >>>> the R coding after taking user's query (who don't have knowledge of R) >>>> in >>>> any format. Can you suggest some language or software made for this >>>> purpose >>>> and is used commonly. >>>> Any kind of help will be appreciable. >>>> -- >>>> Ankhee Dutta >>>> project trainee, >>>> JNU,New Delhi-67 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> Bioconductor mailing list >>>> Bioconductor@stat.math.ethz.ch >>>> https://stat.ethz.ch/mailman/listinfo/bioconductor >>>> Search the archives: >>>> http://news.gmane.org/gmane.science.biology.informatics.conductor >>>> >>>> >>> >>> >>> >>> >> >> -- >> Ankhee Dutta >> project trainee, >> JNU,New Delhi-67 >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> Bioconductor mailing list >> Bioconductor@stat.math.ethz.ch >> https://stat.ethz.ch/mailman/listinfo/bioconductor >> Search the archives: >> http://news.gmane.org/gmane.science.biology.informatics.conductor >> > > Michael Dondrup, Ph.D. > Bergen Center for Computational Science > Computational Biology Unit > Unifob AS - Thormøhlensgate 55, N-5008 Bergen, Norway > Phone: +47 55584029 Fax: +47 55584295 > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Sean Davis21k
For what it is worth, the GGtools package has inst/GGEXsite that includes material that works with CGIwithR to provide the query resolution/graphics functionality visible at www.ggexplorer.org The code driving the web facility was not kept up to date with GGtools so you would have to go back to bioconductor 2.1 to get this thing to work "out of the box". But this gives some sense of what it is like to work with CGIwithR to offer users a regimented query composition system with answers computed by R/bioconductor. On Tue, Sep 8, 2009 at 7:46 AM, Sean Davis<seandavi at="" gmail.com=""> wrote: > On Tue, Sep 8, 2009 at 7:40 AM, Michael Dondrup <michael.dondrup at="" bccs.uib.no="">> wrote: > >> The choice of the appropriate language to build a user interface depends on >> - your skills in the programming languages >> - your requirements, e.g. full blown AJAX web 2.0 with virtual desktop in >> the browser behavior vs. single CGI page >> - ?availability of libraries for user-interfaces meeting these requirements >> I don't know about the first two points, maybe you should figure that out. >> but the UI doesn't come for free with any language solution and its >> construction >> might outweigh the implementing of the analysis. >> > > I would echo these points and add that before doing such a task using R, it > is probably worthwhile being pretty familiar with CGI/web applications, > HTML, server-side versus client-side technologies, etc. ?This is probably > best accomplished in perl/python only because the documentation/literature > is rich. ?When you ?know about handling requests and generating responses, > using R to do so or using a language binding to R can be less challenging, > as the dynamics of web interaction can be quite challenging to grasp early > on. > > >> >> IMHO there are much better languages with support for building >> web-interfaces than R. The CGIwithR package could >> still work, but it has not been updated since 2005, I haven't tried it. >> Maybe the RApache package suggested by Steve is worth a try, too. >> >> If using a different prog. language you always need a sort of language >> binding such that you can call R functions in Perl, Python or Java (e.g. >> RSPerl, rJava, RPy, or transfer via tmpfiles, system commands), that doesn't >> give you the UI magically. Building small web-apps in Perl is quite straight >> forward though, for bigger ones I would (nowadays) try something else. >> >> Am 08.09.2009 um 06:21 schrieb ankhee dutta: >> >> >> ?Thanks for replying Michael but sorry to say that i don't have much >>> knowledge about java and its applications but you were also suggesting to >>> use RSPerl, so will that solve my purpose of making web interface to the R >>> coding, otherwise can i use CGIwithR package for the purpose, how is it >>> and >>> is this package common in use? >>> Please do reply. >>> On Mon, Sep 7, 2009 at 7:01 PM, Michael Dondrup < >>> Michael.Dondrup at bccs.uib.no >>> >>>> wrote: >>>> >>> >>> ?Hi Ankhee, >>>> depends mainly on your favorite host language I think. Among other >>>> suggestions (RPy), I think one of the most commonly used solution is >>>> Java and the rJava package. That can be installed from CRAN. >>>> >>>> That contains JRI so you can run R code from Java (and vice versa), I >>>> ?know >>>> some people that use rJava, and I do, it has little documentation but >>>> otherwise it works fine, and I think the Eclipse R plugin uses it too. >>>> Then >>>> you could build your web UI in Java using eg. JSF, Echo2, or ICEFaces. >>>> >>>> If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or >>>> try a patched version >>>> >>>> >>>> http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl >>>> where we have tried solve some issues. That worked for me at least on a >>>> variety of systems. But maybe noone else is using that. >>>> I don't like the ?"write script to temporary file and pass around tables >>>> in >>>> textfiles" approach too much, I thinks it's not a real clean and not very >>>> efficient approach. But that's only my 50cent ;) >>>> >>>> Michael >>>> >>>> Am 07.09.2009 um 12:24 schrieb ankhee dutta: >>>> >>>> hi all, >>>> >>>>> here i have done some coding in R and want a web interface which can >>>>> execute >>>>> the R coding after taking user's query (who don't have knowledge of R) >>>>> in >>>>> any format. Can you suggest some language or software made for this >>>>> purpose >>>>> and is used commonly. >>>>> Any kind of help will be appreciable. >>>>> -- >>>>> Ankhee Dutta >>>>> project trainee, >>>>> JNU,New Delhi-67 >>>>> >>>>> ? ? ?[[alternative HTML version deleted]] >>>>> >>>>> _______________________________________________ >>>>> 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 >>>>> >>>>> >>>> >>>> >>>> >>>> >>> >>> -- >>> Ankhee Dutta >>> project trainee, >>> JNU,New Delhi-67 >>> >>> ? ? ? ?[[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> Michael Dondrup, Ph.D. >> Bergen Center for Computational Science >> Computational Biology Unit >> Unifob AS - Thorm?hlensgate 55, N-5008 Bergen, Norway >> Phone: +47 55584029 Fax: +47 55584295 >> >> >> _______________________________________________ >> 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 >> > > ? ? ? ?[[alternative HTML version deleted]] > > > _______________________________________________ > 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 > -- Vincent Carey, PhD Biostatistics, Channing Lab 617 525 2265
ADD REPLYlink written 10.2 years ago by Vincent J. Carey, Jr.6.3k
Hi Vince, Vincent Carey wrote: > For what it is worth, the GGtools package has inst/GGEXsite that > includes material > that works with CGIwithR to provide the query resolution/graphics > functionality visible at www.ggexplorer.org I tried to look at this but got Failed to Connect Firefox can't establish a connection to the server at www.ggexplorer.org. Cheers, H. > > The code driving the web facility was not kept up to date with GGtools > so you would > have to go back to bioconductor 2.1 to get this thing to work "out of > the box". But this > gives some sense of what it is like to work with CGIwithR to offer > users a regimented > query composition system with answers computed by R/bioconductor. > > On Tue, Sep 8, 2009 at 7:46 AM, Sean Davis<seandavi at="" gmail.com=""> wrote: >> On Tue, Sep 8, 2009 at 7:40 AM, Michael Dondrup <michael.dondrup at="" bccs.uib.no="">>> wrote: >>> The choice of the appropriate language to build a user interface depends on >>> - your skills in the programming languages >>> - your requirements, e.g. full blown AJAX web 2.0 with virtual desktop in >>> the browser behavior vs. single CGI page >>> - availability of libraries for user-interfaces meeting these requirements >>> I don't know about the first two points, maybe you should figure that out. >>> but the UI doesn't come for free with any language solution and its >>> construction >>> might outweigh the implementing of the analysis. >>> >> I would echo these points and add that before doing such a task using R, it >> is probably worthwhile being pretty familiar with CGI/web applications, >> HTML, server-side versus client-side technologies, etc. This is probably >> best accomplished in perl/python only because the documentation/literature >> is rich. When you know about handling requests and generating responses, >> using R to do so or using a language binding to R can be less challenging, >> as the dynamics of web interaction can be quite challenging to grasp early >> on. >> >> >>> IMHO there are much better languages with support for building >>> web-interfaces than R. The CGIwithR package could >>> still work, but it has not been updated since 2005, I haven't tried it. >>> Maybe the RApache package suggested by Steve is worth a try, too. >>> >>> If using a different prog. language you always need a sort of language >>> binding such that you can call R functions in Perl, Python or Java (e.g. >>> RSPerl, rJava, RPy, or transfer via tmpfiles, system commands), that doesn't >>> give you the UI magically. Building small web-apps in Perl is quite straight >>> forward though, for bigger ones I would (nowadays) try something else. >>> >>> Am 08.09.2009 um 06:21 schrieb ankhee dutta: >>> >>> >>> Thanks for replying Michael but sorry to say that i don't have much >>>> knowledge about java and its applications but you were also suggesting to >>>> use RSPerl, so will that solve my purpose of making web interface to the R >>>> coding, otherwise can i use CGIwithR package for the purpose, how is it >>>> and >>>> is this package common in use? >>>> Please do reply. >>>> On Mon, Sep 7, 2009 at 7:01 PM, Michael Dondrup < >>>> Michael.Dondrup at bccs.uib.no >>>> >>>>> wrote: >>>>> >>>> Hi Ankhee, >>>>> depends mainly on your favorite host language I think. Among other >>>>> suggestions (RPy), I think one of the most commonly used solution is >>>>> Java and the rJava package. That can be installed from CRAN. >>>>> >>>>> That contains JRI so you can run R code from Java (and vice versa), I >>>>> know >>>>> some people that use rJava, and I do, it has little documentation but >>>>> otherwise it works fine, and I think the Eclipse R plugin uses it too. >>>>> Then >>>>> you could build your web UI in Java using eg. JSF, Echo2, or ICEFaces. >>>>> >>>>> If you like perl you might try RSPerl http://www.omegahat.org/RSPerl/ or >>>>> try a patched version >>>>> >>>>> >>>>> http://www.cebitec.uni- bielefeld.de/groups/brf/software/wiki/HowToInstallRSPerl >>>>> where we have tried solve some issues. That worked for me at least on a >>>>> variety of systems. But maybe noone else is using that. >>>>> I don't like the "write script to temporary file and pass around tables >>>>> in >>>>> textfiles" approach too much, I thinks it's not a real clean and not very >>>>> efficient approach. But that's only my 50cent ;) >>>>> >>>>> Michael >>>>> >>>>> Am 07.09.2009 um 12:24 schrieb ankhee dutta: >>>>> >>>>> hi all, >>>>> >>>>>> here i have done some coding in R and want a web interface which can >>>>>> execute >>>>>> the R coding after taking user's query (who don't have knowledge of R) >>>>>> in >>>>>> any format. Can you suggest some language or software made for this >>>>>> purpose >>>>>> and is used commonly. >>>>>> Any kind of help will be appreciable. >>>>>> -- >>>>>> Ankhee Dutta >>>>>> project trainee, >>>>>> JNU,New Delhi-67 >>>>>> >>>>>> [[alternative HTML version deleted]] >>>>>> >>>>>> _______________________________________________ >>>>>> 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 >>>>>> >>>>>> >>>>> >>>>> >>>>> >>>> -- >>>> Ankhee Dutta >>>> project trainee, >>>> JNU,New Delhi-67 >>>> >>>> [[alternative HTML version deleted]] >>>> >>>> _______________________________________________ >>>> 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 >>>> >>> Michael Dondrup, Ph.D. >>> Bergen Center for Computational Science >>> Computational Biology Unit >>> Unifob AS - Thorm?hlensgate 55, N-5008 Bergen, Norway >>> Phone: +47 55584029 Fax: +47 55584295 >>> >>> >>> _______________________________________________ >>> 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 >>> >> [[alternative HTML version deleted]] >> >> >> _______________________________________________ >> 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 >> > > > -- Hervé Pagès Program in Computational Biology Division of Public Health Sciences Fred Hutchinson Cancer Research Center 1100 Fairview Ave. N, M2-B876 P.O. Box 19024 Seattle, WA 98109-1024 E-mail: hpages at fhcrc.org Phone: (206) 667-5791 Fax: (206) 667-1319
ADD REPLYlink written 10.2 years ago by Hervé Pagès ♦♦ 14k
Answer: regarding web interface to R coding
0
gravatar for Shameer Khadar
10.2 years ago by
Shameer Khadar30 wrote:
Hello, Earlier I have tried to use RSPerl / Statistics::R for similar purpose (but had several issues in implementing it). When I asked about similar question on BioPerl list, Jason Stajich suggested me to hack R in a way to create temporary R scripts using Perl and run the script using `R --no-save < tempdir/tempscript.R`. Later you can pipe output file or read up in to your html file using a CGI script. Link to my old post and suggestion by Stajich is here : http://www.nabble.com/Re%3A-Heat-map-module---p21416644.html Trust this helps, Khader Shameer On Mon, Sep 7, 2009 at 3:54 PM, ankhee dutta <ankheedutta@gmail.com> wrote: > hi all, > here i have done some coding in R and want a web interface which can > execute > the R coding after taking user's query (who don't have knowledge of R) in > any format. Can you suggest some language or software made for this purpose > and is used commonly. > Any kind of help will be appreciable. > -- > Ankhee Dutta > project trainee, > JNU,New Delhi-67 > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD COMMENTlink written 10.2 years ago by Shameer Khadar30
Python has an extremely straighforward interface to R called RPy. Python is a very good scripting language for CGI. -Paul. On Mon, Sep 7, 2009 at 12:43 PM, Shameer Khadar <skhadar@gmail.com> wrote: > Hello, > > Earlier I have tried to use RSPerl / Statistics::R for similar purpose (but > had several issues in implementing it). > When I asked about similar question on BioPerl list, Jason Stajich > suggested me to hack R in a way to create temporary R scripts using Perl > and > run the script using `R --no-save < tempdir/tempscript.R`. Later you can > pipe output file or read up in to your html file using a CGI script. > > Link to my old post and suggestion by Stajich is here : > http://www.nabble.com/Re%3A-Heat-map-module---p21416644.html > > Trust this helps, > Khader Shameer > > > On Mon, Sep 7, 2009 at 3:54 PM, ankhee dutta <ankheedutta@gmail.com> > wrote: > > > hi all, > > here i have done some coding in R and want a web interface which can > > execute > > the R coding after taking user's query (who don't have knowledge of R) in > > any format. Can you suggest some language or software made for this > purpose > > and is used commonly. > > Any kind of help will be appreciable. > > -- > > Ankhee Dutta > > project trainee, > > JNU,New Delhi-67 > > > > [[alternative HTML version deleted]] > > > > _______________________________________________ > > Bioconductor mailing list > > Bioconductor@stat.math.ethz.ch > > https://stat.ethz.ch/mailman/listinfo/bioconductor > > Search the archives: > > http://news.gmane.org/gmane.science.biology.informatics.conductor > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor@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 School of Mathematics, Statistics and Applied Mathematics National University of Ireland Galway Ireland [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Paul Geeleher1.3k
You might want to have a look at RGG, R Gui Generator, at http:// rgg.r-forge.r-project.org/ I haven't tried it myself though, so I don't know how well it works. \Heidi On 7 Sep 2009, at 12:49, Paul Geeleher wrote: > Python has an extremely straighforward interface to R called RPy. > Python is > a very good scripting language for CGI. > > -Paul. > > On Mon, Sep 7, 2009 at 12:43 PM, Shameer Khadar <skhadar at="" gmail.com=""> > wrote: > >> Hello, >> >> Earlier I have tried to use RSPerl / Statistics::R for similar >> purpose (but >> had several issues in implementing it). >> When I asked about similar question on BioPerl list, Jason Stajich >> suggested me to hack R in a way to create temporary R scripts >> using Perl >> and >> run the script using `R --no-save < tempdir/tempscript.R`. Later >> you can >> pipe output file or read up in to your html file using a CGI script. >> >> Link to my old post and suggestion by Stajich is here : >> http://www.nabble.com/Re%3A-Heat-map-module---p21416644.html >> >> Trust this helps, >> Khader Shameer >> >> >> On Mon, Sep 7, 2009 at 3:54 PM, ankhee dutta <ankheedutta at="" gmail.com=""> >> wrote: >> >>> hi all, >>> here i have done some coding in R and want a web interface which can >>> execute >>> the R coding after taking user's query (who don't have knowledge >>> of R) in >>> any format. Can you suggest some language or software made for this >> purpose >>> and is used commonly. >>> Any kind of help will be appreciable. >>> -- >>> Ankhee Dutta >>> project trainee, >>> JNU,New Delhi-67 >>> >>> [[alternative HTML version deleted]] >>> >>> _______________________________________________ >>> 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 >>> >> >> [[alternative HTML version deleted]] >> >> _______________________________________________ >> 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 > School of Mathematics, Statistics and Applied Mathematics > National University of Ireland > Galway > Ireland > > [[alternative HTML version deleted]] > > _______________________________________________ > 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
ADD REPLYlink written 10.2 years ago by Heidi Dvinge2.0k
> Python has an extremely straighforward interface to R called RPy. > Python is a very good scripting language for CGI. Also, if you're going that route, Django is a good python based web framework which is real easy to pick up & start using.
ADD REPLYlink written 10.2 years ago by Jeff Gentry3.9k
Jeff Gentry wrote: >> Python has an extremely straighforward interface to R called RPy. >> Python is a very good scripting language for CGI. > > Also, if you're going that route, Django is a good python based web > framework which is real easy to pick up & start using. > If still going the Python/web route, rpy2 is quite multithread- friendly and should accommodate stacks making use of it (apache/mod_python for example).
ADD REPLYlink written 10.2 years ago by laurent140
Hello Ankhee, Please do let us know, what you are finally using for you web application. Cheers, Shameer Khader On Wed, Sep 9, 2009 at 4:15 PM, Laurent Gautier <lgautier@gmail.com> wrote: > Jeff Gentry wrote: > >> Python has an extremely straighforward interface to R called RPy. >>> Python is a very good scripting language for CGI. >>> >> >> Also, if you're going that route, Django is a good python based web >> framework which is real easy to pick up & start using. >> >> > If still going the Python/web route, rpy2 is quite multithread- friendly and > should accommodate stacks making use of it (apache/mod_python for example). > > > _______________________________________________ > Bioconductor mailing list > Bioconductor@stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: > http://news.gmane.org/gmane.science.biology.informatics.conductor > [[alternative HTML version deleted]]
ADD REPLYlink written 10.2 years ago by Shameer Khadar30
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