From kchine at ebi.ac.uk  Mon Nov 19 22:42:20 2007
From: kchine at ebi.ac.uk (kchine at ebi.ac.uk)
Date: Mon, 19 Nov 2007 21:42:20 -0000 (GMT)
Subject: [Rd] biocep project - R for the Web and the Virtual R Workbench
Message-ID: <33033.172.188.210.62.1195508540.squirrel@webmail.ebi.ac.uk>

Dear all,

I have been writing during last year at the European Bioinformatics
Institute a general unified open source solution for R integration. This
work is now available via this link:
http://www.ebi.ac.uk/microarray-srv/frontendapp/
The different frameworks and tools of the biocep project are now robust
enough for production use. The different APIs are finalized but the
documentation is incomplete.
the last version of the biocep README file can be found here :
http://www.ebi.ac.uk/microarray-srv/frontendapp/BIOCEP_README.txt

Here are the major use cases I dealt with :

- Generate java mappings for R Objects (Standard/S4).
- Generate java mappings for selected packages' functions
(Generic/TypeInfoed).
- Use R and the R packages as a Java Toolkit via a Rich, High level,
Object-Oriented API.
- Deploy and use R as a remote component.
- Expose automatically R packages and the R API as JAX-WS stateless or
statefull Web Services.
- Use R within a resource pooling infrastructure for scalable, web
oriented, data analysis applications.
- Use the Remote Resources Pooling framework (RPF) to deploy and use
distributed computational resources (non R based, native libraries with
JNI support or java code)
- Use R for parallel computing via  a Java API or Web Services.
- Create and use Remote R Instances from within R (snow' like fucntions :
makeCluster, clusterEvalQ, clusterExport, clusterApply,  stopCluster ..)
- Use the R API from within an applet (book, use and release a Remote R
Instance via HTTP Tunneling)
- Use R to generate Graphics on the fly for thin web clients
- Use R from within a Workbench that includes an advanced script editor, 
a Spreadsheet View fully connected to R data and functions, an R Object
Inspector,
composable and dockable Views, interactive R devices, clonable R Graphics..
- Use the Workbench from within a browser or via Java Web Start to access
a pool of Remote R Instances
- Use the Workbench to control on demand any Remote R Instance
- Provide a packaging for R Based Desktop applications that enables Web
based, one click installation (Embedded R for Windows, detected R for
other operating systems)

This work uses extensively a large number of existing open source projects
as is or patched.

The public SVN url/login/pasword for the biocep project are in the README
file

You may want to try the Virtual R Workbench on your local machine, use the
following link :  
http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp
or type 'javaws
http://www.ebi.ac.uk/microarray-srv/frontendapp/rworkbench.jnlp' from the
command line.
This is a one click installation process for Windows and Mac OS X. (You
need to preinstall R on Mac OS X while on Widows an embedded R 2.6 can be
deployed and used)
The Java Web Start installer creates an RWorkbench directory in your home
dir with all the files required. You may continue launching the
application via the url (good for fetching updates automatically)
or use the RWorkbench/VRWorkbench.txt to Run the application off line.
rename it to VRWorkbench.bat on Windows or type 'source VRWorkbench.txt'
on Mac OS X command line.
use the sources of biocep to run the R Workbench on Unix-like operating
systems.

Best wishes,

Karim



[Rd] biocep project - R for the Web and the Virtual R Workbench
kchine at ebi.ac.uk