E.coli_iJR904 {BiGGR} | R Documentation |
An expanded genome-scale model of Escherichia coli K-12 (iJR904
GSM/GPR). 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(E.coli_iJR904)
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
Reed, J.L., Vo, T.D., Schilling, C.H., and Palsson, B.O., An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR), Genome Biology, 4(9): R54.1-R54.12 (2003).
## 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) E.coli_iJR904 <- rsbml_read(text=string) ## End(Not run) ##load data and get all reaction IDs data(E.coli_iJR904) model <- E.coli_iJR904@model ##get all reaction identifiers sapply(model@reactions, id)