R Portal

The upcoming BiG Grid R portal

To make using the grid easier, we're working a portal for users of the statistical programming language R. It's a web interface for your jobs, and a module for R. Plus some tools and language bindings to interact with the jobs.

As a bonus, you can also use it to run R on a GPU cluster.

The R portal is not a production service yet. We're currently looking for R users who want to help us to make it work smoothly in a real-world setting. If you're interested, please drop me a mail.

• Visit the R portal (contact wvengen+lgi@nikhef.nl for an account)
• read more about the Rlgi module for R.
• Slides of the R portal presentation at the BioAssist meeting of Feb, 2012.

What's inside

The system is based on the Leiden Grid Intrastructure (LGI). It interacts with the grid using pilotjobs (read more).

• Leiden Grid Infrastructure(original source), including a number of tools
• lgipilot pilotjob manager
• R portal source

On the grid, R 2.11 and 2.12 are available; the gpu cluster has versions 2.12 and 2.13.

Packages installed on the grid: affy affydata affyio affyPLM affyQCReport annaffy annotate base biomaRt bitops boot class cluster codetools datasets foreign gcrma genefilter geneplotter graphics grDevices grid hgu95av2.db IRanges KEGG.db KernSmooth lattice limma marray MASS Matrix methods mgcv multtest nlme nnet org.Hs.eg.db preprocessCore RColorBrewer RCurl Rlgi rpart RSQLite simpleaffy spatial splines stats stats4 survival tcltk tools utils vsn XML xtable
Packages on the GPU cluster: base bitops boot class cluster codetools datasets foreign graphics grDevices grid KernSmooth lattice MASS Matrix methods mgcv nlme nnet Rcpp rgpu rgputools rpart snow spatial splines stats stats4 survival tcltk tools utils XML
(you can still use install.packages() to install extra packages right now)