M.barkeri_iAF692 {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(M.barkeri_iAF692)
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
Feist, A.M., Scholten, J.C.M., Palsson, B.O., Brockman, F.J., and Ideker, T., "Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri", Molecular Systems Biology, 2(1):msb4100046-E1-E14 (2006)
## 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) M.barkeri_iAF692 <- rsbml_read(text=string) ## End(Not run) ##load data and get all reaction IDs data(M.barkeri_iAF692) model <- M.barkeri_iAF692@model ##get all reaction identifiers sapply(model@reactions, id)