search for: biocep

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 : -...

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 : - Ge...

> > > Dear All, I just posted an interview with Karim Chine of http://www.biocep.net/ who has successfully built a latform for on demand data mining enabled by the cloud through R. Here is an except BIOCEP is built on top of R and Scilab and anything that you can do within those environments is accessible through BIOCEP. Here is what you have uniquely with this new R/Scilab-b...

...at this, so I hope you ask me for specific details that are necessary) Some of the things that we had unsuccessfully tried included playing around with: 1) CGIwithR package: This package appeared to be geared for Unix / Apache systems, so we couldn't get too far in the Windows Environment. 2) Biocep.net : We tried to use the tools from biocep.net to generate SOAP service definitions for R functions. We followed the instructions on biocep.net but we couldn't run the java program to access the R-soap from java. It would be great if someone in the group has had success in implementing R-Soa...

Hello, Earlier I posted a question about memory usage, and the community's input was very helpful. However, I'm now extending my dataset (which I use when running a regression using lm). As a result, I am continuing to run into problems with memory usage, and I believe I need to shift to implementing the analysis on a different system.. I know that R supports R servers through

...mo). And of course this is cross platform, the R client can be 32 bit windows, the R server can be 64 bit lunix. Or remote graphics for example. So I'm looking to do the same as the demo, but with a binary socket. Does anyone have any ideas? I've looked a bit at Rserve, bigmemory, biocep, nws but although all those packages are great, I didn't find anything that worked in exactly this way i.e. i) R to R ii) CLI non-blocking and iii) no need to startup R in a special way Regards, Matthew

...apturar el "device" donde R dibuja su salida directamente en el GUI que diseño con Java (sin guardar el fichero .png, cargarlo desde Java, etc.). ¿Alguien se ha enfrentado antes con este problema? No he visto referencias en ningún sitio aunque me consta que zambulléndome en el código de Biocep, JGR u otros proyectos análogos podría encontrar una respuesta... Un saludo, Carlos J. Gil Bellosta

Hi, I'm planning to embed R into an application, with the following context: - This application is written in Java (and managed with maven). I plan accessing R using JRI. - This application must be installable on several plateform (linux, mac os, windows). - The R engine must embed library, some of them having native code in C or Fortran. Does this sound reasonable? I would be very

Hello, I am interesting in using R from a web application, for basic statistics and plots. The server is Java-based (tomcat). The simplest solution is a system call that generates the text or the image, then the servlet forwards the output. This can be done from any language, but it is quite inelegant and slow for the initialization time. Is there any package or approach for accessing R from a

Hello, we are writing rich internet user interfaces and like to call R for some of the computational needs on the data, as well as some creation of image files. Our objects communicate via the SOAP interface. We have been researching the various packages to expose R as a SOAP service. No current CRAN SOAP packages however. Found 3 to date: RSOAP (http://sourceforge.net/projects/rsoap/)

Hi All, I was wondering if anybody had experience running R on amazon's ec2 "cloud"? More specifically, has anybody created an "amazon machine image" (AMI) for use with it? I was wondering if there was a quantian type image available as an amazon machine image, maybe running debian or ubuntu? It supports open MPI among other libs which is nice. It would be nice to put

...e predicted values. I necessarily have to use FLEX for the interface. In trying to make sense of how to go about this task, I have speculated on the following technologies: 1) Using RSOAP which requires a Python client. I am not sure how I can implement this in Flex. 2) Using RSOAP provided by the Biocep project. This is a java implementation and maybe this would suit my requirements. 3) The StatDataML package in R provides the creation of xml files of R objects. Maybe I can use these XML files as encapsulators of R object data and pass it on to FLEX. 4) Since R has interfaces that connect to most...

...alization more rich and dynamic) is to use Adobe FLEX front end and communicate with R using the RSOAP library. There is very sparse documentation relevant to using RSOAP. I have not been able to find examples or tutorials using RSOAP. Any information in this regard will be highly appreciated. The Biocep project provides 'R for cloud computing' but unfortunately I have not been able to extract relevant 'juice' from their webpage. What i did get is their R workbench, but that has not answered my above mentioned queries. Regards, Harsh Singhal

Hello, I am new to R and have created an application using R 2.10, with a graphical UI using TclTk 8.5, running on windows 7, quad core machine. The intention of the application is to launch calculations and display results on a graphical dashboard. I've reached a roadblock, and I need to confirm that the following CANNOT be done. I've been trying to find a mechanism for doing the

Hi everyone, Has anyone written a parser in Java for either the ASCII or binary format produced by save()? I need to parse a single large 2D array that is structured like this: list( "32609_1" = c(-9549.39231289146, -9574.07159324482, ... ), "32610_2" = c(-6369.12526971635, -6403.99620977124, ... ), "32618_2" = c(-2138.29095689061, -2057.9229403233, ... ),

...-c it) Elsewhere... http://linuxmachine:8675/htmlDF?theData -> HTML table version of data frame or http://linuxmachine:8675/csvDF?theData -> CSV export of data frame Then I C-c my server and continue working in R. Rserve has its own protocol, plus it spawns extra processes. biocep looks interesting, but it's far more ambitious than this, and I can't tell if it would actually work in this case. svSocket looks interesting, but (if I understand it correctly) it would be a lot of work to implement HTTP over its raw sockets. Basically, I have a few tools (including Exce...

Hi 2 questions- 1. Is there a package that will allow me to run R scripts (entirely) from Java? 2. If so, is there a way to capture the output of those scripts, (including images) and embed them in my SWT java app? My challenge is I have a java app that does some statistical chores- it would be fantastic if the users could use their R skills to modify a script in whatever R environment they like

Hey guys, I'm a (Java) integration architect. We are currently stuck with SAS but I'd be happy to switch that to R! (of course ;-). Now, a big argument for the latter, is that we can integrate it seamlessly with all our existing (java) apps. Therefore: has anyone heard of a java API (like SAS has it's Java API for enterprise integration) or a Service we can call (e.g. a web service,

Has anyone come across any alternatives to rJava and JRI? Are they any good? Better perhaps? Please give your reasons. Thanks, Danish - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - This message is intended only for the personal and confidential use of the designated recipient(s) named above. If you are not the intended recipient of this message you are

Does anyone know a way that an function written in R can be called within a cell of an Excel spreadsheet. I would like to use the R function much as I use the native Excel functions, e.g. instead of using the excel function sum, =sum(A2,A6), I would like to use the function mysum written in R, e.g. =mysum(A2,A6). Thanks, John John Sorkin M.D., Ph.D. Chief, Biostatistics and Informatics