M.barkeri_iAF692: Metabolic reconstruction of M.barkeri from the BiGG database

In hettling/BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description

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.

Usage

data(M.barkeri_iAF692)

Format

An sbml object of class rsbml

Details

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).

Source

http://bigg.ucsd.edu/bigg/exportSelect.pl

References

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)

Examples

## 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)

hettling/BiGGR documentation built on April 17, 2020, 5:19 a.m.