MIDIA Software (v1.1)


INSTALLATION


MIDIA requires R version 2.11.1 or higher. For download, installation and documentation for R, see CRAN.

Installation of supporting R packages

The following R packages must be correctly installed and must reside in the /library directory (or 'folder') within R: gRbase and Rgraphviz (together with all R packages on which these in turn depend, including in particular the R packages graph, RBGL, MASS, and grid).
The package rsbml should also be installed by users who wish to import SBML models into MIDIA.

The package rsbml is an R binding for libsbml available within Bioconductor's biocLite. Information, downloads and documentation for the 3 packages are available from the following links: gRbase, Rgraphviz, rsbml.

A straightforward way to perform the package installations is to enter the commands:
install.packages(c("graph","gRbase"))
source("http://www.bioconductor.org/biocLite.R")
biocLite("Rgraphviz")
biocLite("rsbml")

Loading MIDIA

The MIDIA package is loaded in 2 stages. First, load the latest version of the MIDIA R workspace .zip .tar.gz. Second, load the supporting R packages gRbase and Rgraphviz (ensuring that these have already been installed, as described in the preceding section). The necessary commands for the first R session using MIDIA are (assuming that the .RData file resides in a directory called /MIDIA):

load("/MIDIA/MIDIAbeta1.1.RData")
library(gRbase)
library(Rgraphviz)

The .Rdata file loaded at the start of subsequent sessions should be chosen appropriately by the user, and must always include all objects contained in the original MIDIA R workspace. A convenient approach is to expand the original MIDIA workspace with the user's own objects, always saving the workspace at the end of one session and reloading the same workspace at the start of the next. The supporting R packages gRbase and Rgraphviz are automatically loaded when the MIDIA(.) function is called. It is recommended when working with MIDIA always to set the current R directory to /MIDIA.

Functions, help and source code

Users requiring help for a given function may consult the function description and script within R by simply typing the function name (e.g. by typing mRmSmPfromSBML for the function used to import SBML models to MIDIA, or by typing MIDIA for the main function).

The subsequent sections of this Supplementary Material contain extensive description of the MIDIA(.) function itself, including tutorial examples, an overview of how to use the function, and documentation concerning its input variables and outputs.

All source code for the MIDIA package is provided as a collection of .R scripts for advanced users zip tar.gz.
Such users may wish to edit and extend the component R functions they contain. (The source(.) command must then be used to incorporate the new version of each edited .R file into the workspace).

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