S.cerevisiae_iND750 {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.cerevisiae_iND750)
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
Duarte, N.C., Herrgard, M.J., and Palsson, B.O., " Reconstruction and Validation of Saccharomyces cerevisiae iND750, a Fully Compartmentalized Genome-scale Metabolic Model", Genome Research, 14: 1298-1309 (2004)
## 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.cerevisiae_iND750 <- rsbml_read(text=string) ## End(Not run) ##load data and get all reaction IDs data(S.cerevisiae_iND750) model <- S.cerevisiae_iND750@model ##get all reaction identifiers sapply(model@reactions, id)