R: Metabolic reconstruction of M.tuberculosis from the BiGG...
M.tuberculosis_iNJ661
R Documentation
Metabolic reconstruction of M.tuberculosis from the BiGG database
Description
A metabolic reconstruction for tuberculosis.
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.tuberculosis_iNJ661)
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., Henry, C.S., Reed, J.L., Krummenacker, M., Joyce, A.R., Karp, P.D., Broadbelt, L.J., Hatzimanikatis, V., Palsson, B.O.,
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information, olecular Systems Biology, 3:121 (2007)
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.tuberculosis_iNJ661 <- rsbml_read(text=string)
## End(Not run)
##load data and get all reaction IDs
data(M.tuberculosis_iNJ661)
model <- M.tuberculosis_iNJ661@model
##get all reaction identifiers
sapply(model@reactions, id)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(BiGGR)
Error in library(BiGGR) : there is no package called 'BiGGR'
Execution halted