[Bioc-devel] R web interface (Sjoerd Vosse)

[Stefan McKinnon Høj-Edwards]

Hi,

You might want to look into RStudio.org, which has a web-interface for their IDE application ("RStudio Server").
Not quite what you are asking for, but I am thinking you could use it as a framework and add a nice GUI for your project.

Kind regards

Stefan McKinnon Høj-Edwards              Dept. of Molecular Biology and Genetics
Ph.D. Fellow                             Aarhus University
                                         Blichers Allé 20, Postboks 50
                                         DK-8830 Tjele
Tel.: +45 8715 7969                      Tel.: +45 8715 6000
Email: Stefan.Hoj-Edwards at agrsci.dk      Web: www.agrsci.dk



> -----Oprindelig meddelelse-----
> Date: Tue, 7 Aug 2012 03:26:45 -0700 (PDT)
> From: Sjoerd Vosse <sjoerdvos at yahoo.com>
> To: "bioc-devel at r-project.org" <bioc-devel at r-project.org>
> Subject: [Bioc-devel] R web interface
> Message-ID:
> 	<1344335205.11396.YahooMailNeo at web114704.mail.gq1.yahoo.com>
> Content-Type: text/plain
> 
> First of all, I'm not sure if this is the right mailing list for this
> question. If not, I would appreciate anyone telling me so :)
> 
> 
> Dear R developers,
> 
> a few years ago I developed an online R interface (OnlineR) for a
> microarray institution in the Netherlands. I am now thinking of
> extending and publishing this online application, but I would first
> like to hear your thoughts on whether there would be a demand for such
> an application, and if it does not already exist. I checking the R-Web-
> Interfaces page, but I did not find anything as flexible, user-friendly
> or extended (he said humbly) as my application. Below I will list the
> features and some thoughts, and I would appreciate any feedback anyone
> can offer.
> 
> 1. User management
> 
> This application generally has 3 user groups:
> 
> 
> - Statisticians writing scripts for users
> - End-users (biologists in my case) analysing their data
> - Administrators
> 
> Each kind of group has specific functionality and permissions
> available, which a user with administrative rights can assign to them.
> It is important to note that administrators can give any kind of
> permission to any kind of group or individual users within any group.
> Administrators can also create user groups, or give a user
> administrative rights over a single group for example. I'm just using a
> lot of words here to say that the user permission module is entirely
> flexible.
> 
> 
> 2. File management
> 
> User can upload and manage files in a drag-and-drop file manager.
> Administrative users can assign a quota to other users. When the quote
> is reached no more files can be uploaded or analyses that output files
> to the file manager run. Furthermore, and my users found this a very
> important feature, users can give access to their files to other users
> or groups, be they raw data or analysis results. Share permissions are
> either view, edit or delete or any combination of these.
> 
> 3. Creating analyses
> 
> 
> Users with the proper permissions can create analyses (for lack of a
> better word) for end users. The statistician simply uploads or writes
> an R script and uses the appropriate syntax to define the required user
> input and analysis output, and then defines which users or groups can
> run this script. End-users will have an overview of available analyses
> (organised in categories, sub-categories, or whatever the administrator
> defines) and can run them by simply clicking on them. On the next
> screen they will see an intuitive HTML form asking them for their
> input. When the input has been received (and validated) the R script is
> run in the background. Administrators can give end-users a quota of
> maximum number of analyses they can run simultaneously. The output is
> either printed on the screen, e-mailed or stored in the file manager
> (from whence it can be downloaded), whatever the statistician has
> decided.
> 
> The syntax for the statistician to define the required user input will
> look something like the following:
> 
> name <- '{text;Name;Sjoerd;validation:required:true;}';
> age <- {select;Age;options:30:31:32};
> etc
> 
> User input statements are included between brackets and allow the
> statistician to define the type of input, the required validation and
> the available and default values.
> 
> Input can be any of the available HTML elements, most importantly:
> 
> - input text
> - input textarea
> - upload file
> - radio button
> - dropdown select
> - checkbox
> 
> Statisticians can of course include a description and usage
> descriptions with their script. Also, it will include version
> management, to allow statisticians to update their scripts while still
> allowing end-users to reproduce their previous results with older
> versions of the script.
> 
> 
> 4. User interface
> 
> In my days as a scientific programmer I have noticed that virtually no
> developers take the time to create an eye-pleasing and intuitive user
> interface for the users of the software. I have noticed however, that
> this makes the software look overly complicated and actually frightens
> the less computer-literate users. I will make sure to make this
> application as user-friendly and visually attractive as possible.
> 
> Tools & requirements (nothing surprising here):
> - PHP 5
> - MySQL
> - R
> - HTML, CSS, JavaScript
> - Linux server
> 
> Once again, any feedback would be appreciated. Most of all I'm
> interested to know if you think end-users will appreciate and use the
> above-described web application, and, just as important, if
> statisticians and developers are willing to put in the effort for their
> colleagues ;)
> 
> 
> 
> Kind regards,
> 
> Sjoerd
>