buildSBMLFromBiGG: Build an SBML model from a given reactions file obtained from...
In BiGGR: Constraint based modeling in R using metabolic reconstruction databases

Description Usage Arguments Value Note Author(s) References See Also Examples

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

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

`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`

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

Note that it can be the case that species can be present in multiple compartments. In order to avoid any ambiguities in the model returned by the function, each species identifier is composed of the species identifier given in the reactions file and the compartment identifier, joined by "_". Example: adp in compartment c (cytosol) has the id adp_c.

Anand Gavai, Hannes Hettling

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/

createLIMFromSBML

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