CARMAweb is designed as a multi-tier application based on the J2EE environment, including Java Server Pages and Servlets for the web tier, and Enterprise Java Beans for the middle tier. With the exception of the module for cluster analysis, visualization and classification, all calculations are performed in R using functions of the Bioconductor packages. The connection between Java and R is established through Rserve (). Each analysis is processed in R using the R function Sweave (). Sweave is a tool that allows embedding of R code into LaTeX documents. Sweave executes the R commands from the input file, which is created by the web application. Output from R, R commands and descriptive text are written into a LaTeX file. Thus, code, results and descriptions are presented in a consistent way. After the analysis the LaTeX file generated by Sweave is transformed into a pdf analysis report file. These analysis report files contain all R commands used to perform the analysis, together with descriptions for the various methods used. This guarantees a maximum of transparency and reproducibility of each analysis performed in CARMAweb. The CARMAweb user guide gives a short introduction to the various analysis methods available in the web application. Test datasets are provided for each microarray platform.
The current implementation of CARMAweb runs on a server equipped with two AMD Opteron (64 bit CPU) processors and 4 GB of physical memory. CARMAweb will be updated regularly to the newest R and Bioconductor releases. The current version of CARMAweb uses R version 2.2 and Bioconductor release 1.7.