Description Usage Format Details Source References Examples
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.
1 |
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)
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 | ## 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)
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