[BioC] regarding web interface to R coding

Tue Sep 8 17:07:58 CEST 2009

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]]
>>>>>
>>>>> _______________________________________________
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>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>>
>>>
>>> --
>>> Ankhee Dutta
>>> project trainee,
>>> JNU,New Delhi-67
>>>
>>>        [[alternative HTML version deleted]]
>>>
>>> _______________________________________________
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>>>
>>
>> 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
>>
>>
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>
>        [[alternative HTML version deleted]]
>
>
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-- 
Vincent Carey, PhD
Biostatistics, Channing Lab
617 525 2265