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