toSBML: Export the network to SBML-qual format

In saezlab/CellNOptR: Training of boolean logic models of signalling networks using prior knowledge networks and perturbation data

Export the network to SBML-qual format

Description

Export a Boolean network <network> to an sbml-qual file <fileName>. This file can then be read in using other software that supports SBMLqual standards.

The function also takes a bit string as input. It cuts the model according to the values in bitstrings and write the new model object to SBMLqual.

Usage

toSBML(network, file, bitString = c(rep(1,length(network$reacID))),version=c("standard","cellnopt"))

Arguments

network	a valid CellNOptR network model created by e.g. readSIF()
file	a valid filename to save the SBMLqual model
bitString	optional vector of binary values (for example the resulted bitString from optimisation) to cut the unnecessary interactions from the network before exporting.
version	defines the format of SBMLqual file, read details.

Details

version = "standard" exports one transition block for each node of the network. This format is the SBMLqual standard, that can be imported then with other softwares

version = "cellnopt" the exported file follows a simplified syntax, where each edge of the network is transformed to a transition block in the SBMLqual file. Can be later imported to CellNOptR again.

Author(s)

Francesco Ceccarelli

Examples

  data(ToyModel,package="CellNOptR")
  toSBML(ToyModel,file = tempfile())

saezlab/CellNOptR documentation built on April 16, 2024, 5:21 a.m.