writeSBML: Exports a Metabolic Network in SBML Format

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

View source: R/sybilSBML.R

Description

The function exports a metabolic network from S4 object of the class modelorg in SBML format. The function returns TRUE if the SBML file is successfully built.

Usage

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  writeSBML(morg=NULL,level=2,version=4,fbcLevel=0,
             filename="export.xml",
             recoverExtMet=FALSE,
             printNotes=TRUE,
             printAnnos=TRUE,
             validation=FALSE)

Arguments

morg

An S4 object of the class modelorg.

level

A single integer value containing the SBML level for the exporting SBML file.
Default: 2.

version

A single integer value containing the SBML version for the exporting SBML file.
Default: 4.

fbcLevel

A single integer value containing the fbc package version for the exporting SBML file.
Default: 2.

filename

SBML filename for exporting the model. Default: "export.xml".

recoverExtMet

Boolean: recover external metabolites and refer them to compartment "BOUNDARY".
Default: FALSE.

printNotes

Boolean: print Notes from original SBML file .
Default: TRUE.

printAnnos

Boolean: print Annotations from original SBML file .
Default: TRUE.

validation

Boolean: print containing errors for xml file .
Default: TRUE.

Details

The library libSBML is used to export a modelorg to a SBML file.

Value

A single boolean value for a successful export .

Note

The function writeSBML makes use of the library libSBML (http://www.sbml.org).

Author(s)

Gabriel Gelius-Dietrich <[email protected]>

Maintainer: Claus Jonathan Fritzemeier <[email protected]>

References

The BiGG database http://bigg.ucsd.edu/.

Bornstein, B. J., Keating, S. M., Jouraku, A., and Hucka M. (2008) LibSBML: An API Library for SBML. Bioinformatics 24, 880–881.

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

Becker, S. A., Feist, A. M., Mo, M. L., Hannum, G., Palsson, B. Ø. and Herrgard, M. J. (2007) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox. Nat Protoc 2, 727–738.

Schellenberger, J., Que, R., Fleming, R. M. T., Thiele, I., Orth, J. D., Feist, A. M., Zielinski, D. C., Bordbar, A., Lewis, N. E., Rahmanian, S., Kang, J., Hyduke, D. R. and Palsson, B. Ø. (2011) Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0. Nat Protoc 6, 1290–1307.

See Also

readSBMLmod

Examples

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  dir  <- system.file(package = "sybilSBML", "extdata")
  file <- file.path(dir, "ecoli_core_model.xml")
  mod  <- readSBMLmod(file, bndCond = FALSE)
  writeSBML(mod,level=3,version=1,fbcLevel=2)

sybilSBML documentation built on May 29, 2017, 3:31 p.m.