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
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).
Becker, S.A. and Palsson, B.O., Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation, BMC Microbiology, 5(1):8 (2005)
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## 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) S.aureus_iSB619 <- rsbml_read(text=string) ## End(Not run) ##load data and get all reaction IDs data(S.aureus_iSB619) model <- S.aureus_iSB619@model ##get all reaction identifiers sapply(model@reactions, id)
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