[R] biocep project (R for the Web and the Virtual R Workbench)

[Karim Chine]

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