Karim Chine
2007-Nov-19 19:44 UTC
[R] biocep project (R for the Web and the Virtual R Workbench)
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
elw at stderr.org
2007-Nov-21 14:11 UTC
[R] biocep project (R for the Web and the Virtual R Workbench)
Some of the bits and pieces in this look like very strong candidates for breaking off into CRAN packages, if you haven't done so already. This looks like very nice work - you should be proud! :-) --elijah On Mon, 19 Nov 2007, Karim Chine wrote:> Date: Mon, 19 Nov 2007 19:44:51 +0000 > From: Karim Chine <kchine at ebi.ac.uk> > To: R-help at r-project.org > Subject: [R] biocep project (R for the Web and the Virtual R Workbench) > > 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 > > ______________________________________________ > R-help at r-project.org mailing list > https://stat.ethz.ch/mailman/listinfo/r-help > PLEASE do read the posting guide http://www.R-project.org/posting-guide.html > and provide commented, minimal, self-contained, reproducible code. >