| writeSBMLmod | R Documentation |
Write a model in SBML format
Description
This function converts a data.frame or a modelOrg object to a valid SBML file. The Systems Biology Markup Language (SBML) is a representation format, based on XML, for communicating and storing computational models of biological processes.
Usage
writeSBMLmod(modelData, modelID = "model", outputFile, boundary = "b")
Arguments
modelData |
A modelOrg or a data.frame object. If a data.frame is given, it must contain following mandatory colnames:
-
'ID': A list of single character strings containing the reaction abbreviations, Entries in the field abbreviation are used as reaction ids, so they must be unique.
-
'REACTION': A set of stoichiometric reaction with the following characteristics:
Arrows symbols must be given in the form '=>' or '<=>'
Inverse arrow symbols '<=' or other types as: '-->', '<==>', '->' will not be parsed and will lead to errors.
Arrow symbols and plus signs (+) must be surrounded by a space character
Stoichiometric coefficients must be surrounded by a space character and not by parentheses.
Each metabolite must have only one stoichiometric coefficient, substituents must be joined to metabolite name by a hyphen (-) symbol.
Exchange reactions must have only one metabolite before arrow symbol
Compartments must be given between square brackets ([compartment]) joined at the end of metabolite name
Some examples of valid stoichiometric reactions are:
-
'GPR': A set of genes joined by boolean operators as AND or OR, rules may be nested by parenthesis. (optional: column can be empty),
-
'LOWER.BOUND': A list of numeric values containing the lower bounds of the reaction rates.
If not set, zero is used for an irreversible reaction and -1000 for a reversible reaction. (optional: column can be empty),
-
'UPPER.BOUND': A list of numeric values containing the upper bounds of the reaction rates.
If not set, 1000 is used by default. (optional: column can be empty),
-
'OBJECTIVE': A list of numeric values containing objective values (-1, 0 or 1) for each reaction (optional: column can be empty).
|
modelID |
A single character string giving the modelID
|
outputFile |
A writable path for the output 'SBML' file to be generate
|
boundary |
A single character string specifying the compartment to be used as boundary, 'b' is used by default
|
Value
A valid SBML file
Author(s)
Daniel Camilo Osorio <dcosorioh@tamu.edu>
Examples
# Loading a metabolic model
glycolysis <- read.csv(system.file("extdata/glycolysisModel.csv",package = "minval"), sep='\t')
## Not run:
# Writing a model in SBML format
writeSBMLmod(modelData = glycolysis,modelID = "Glycolysis",outputFile = "glycolysis.xml")
# Writing a modelOrg object in a SBML format
## Loading the sybil R package
library(sybil)
## Loading the data
data("Ec_core")
## Writing the modelOrg object in a SBML format
writeSBMLmod(modelData = Ec_core,modelID = "E.coli",outputFile = "eColi.xml")
## End(Not run)
