writeSBMLmod: Write a model in SBML format
In dosorio/minval: MINimal VALidation for Stoichiometric Reactions

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: `H2O[c] + Urea-1-Carboxylate[c] <=> 2 CO2[c] + 2 NH3[c]` `ADP[c] + Phosphoenolpyruvate[c] => ATP[c] + Pyruvate[c]` `CO2[c] <=>` `'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)

dosorio/minval documentation built on May 24, 2022, 7:42 p.m.