BiGGR (version 1.8.0)

buildSBMLFromBiGG: Build an SBML model from a given reactions file obtained from the BiGG database

Description

Creates an SBML model containing all species, reactions and compartments that occur in a reactions file obtained from the BiGG database.

Usage

buildSBMLFromBiGG(reactions.filename, model.id=character(0), model.name=character(0))

Arguments

reactions.filename

name of the file containing the reactions extracted from BiGG

model.id

id for the SBML model created by the function. Defaults to reactions.filename

model.name

name for the SBML model created by the function. Defaults to reactions.filename

Value

a rsbml Model object containing all reactions, species and compartments that are associated with the reactions in the given input file.

References

Schellenberger, J., Park, J. O., Conrad, T. C., and Palsson, B. , BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions, BMC Bioinformatics, 11:213, (2010). http://bigg.ucsd.edu/

See Also

createLIMFromSBML

Examples

##build model from file Reactions.txt from the package examples  
path <- system.file("extdata", "Reactions.txt", package="BiGGR")
model <- buildSBMLFromBiGG(path, model.id="myid")