[BioC] regarding web interface to R coding

Tue Sep 15 00:04:20 CEST 2009

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]]
>>>>>>
>>>>>> _______________________________________________
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>>>>>> Search the archives:
>>>>>> http://news.gmane.org/gmane.science.biology.informatics.conductor
>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>>
>>>> --
>>>> 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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> 
> 
> 

-- 
Hervé Pagès

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