S.aureus_iSB619 {BiGGR} | R Documentation |
The dataset was generated by downloading the SBML file of the
reconstruction (http://bigg.ucsd.edu/bigg/exportSelect.pl) which was subsequently converted
into an object of class SBML
using the rsbml_read
function
from the rsbml
package.
data(S.aureus_iSB619)
An sbml object of class rsbml
Note that the files in the BiGG database fail the unit
consistancy check of the rsbml_read
function. To avoid
unit checking when creating SBML
objects, the substance units in the reaction tags
were parsed out from the database SBML files (see example below).
http://bigg.ucsd.edu/bigg/exportSelect.pl
Becker, S.A. and Palsson, B.O., Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation, BMC Microbiology, 5(1):8 (2005)
## Not run: ##The dataset was generated as follows: ##SBML_export.xml was downloaded from http://bigg.ucsd.edu/bigg/exportSelect.pl ##and a newline was added at the end of the file file <- "SBML_export.xml" string <- paste(readLines(file), collapse="\n") ##Parse out units to avoid validation error string <- gsub("units=\".+?\"", "", string) S.aureus_iSB619 <- rsbml_read(text=string) ## End(Not run) ##load data and get all reaction IDs data(S.aureus_iSB619) model <- S.aureus_iSB619@model ##get all reaction identifiers sapply(model@reactions, id)