createLIMFromSBML {BiGGR} | R Documentation

## Create a LIM model object from an SBML file

### Description

creates a model file to be run for simulations of metabolic fluxes

### Usage

    createLIMFromSBML(model, maximize, equations=NULL, inequalities=NULL,
    		constraints=NULL, externals=NULL, file.name="model.lim")

### Arguments

`model` | an SBML object of reactions/metabolites participating in a metabolic pathway.
`maximize` | a character vector consisting the tag of the reaction(s) to be maximized or minimized
`equations` | a `list` specifying equality constraints on the system. The list must have two entries, the first one being a vector of class `character` containing the left hand side(s) of the equation(s), the second one being a vector of type `character` or `mumeric` with the right hand side(s) of the equation(s). See also 'examples'.
`inequalities` | a `list` specifying inequality constraints on the system. The list must have three entries, the first one being a vector of class `character` containing the left hand side(s) of the inequality equation(s), the second one being a vector of type `character` or `mumeric` with the right hand side(s) of the inequality equation(s) and the third one being a vector of class `character` containing the relational operator of the inequality equations, for example `">"` or `"<="`. See also 'examples'.
`constraints` | a `list` specifying constrained on the solution space of the flux vector. The list must have three entries, the first one being a vector of class `character` with the reaction id(s) to be constrained, the second and third one a `numeric` vector with the lower and upper flux bounds, respectively, for the reactions to be contrained. is a character vector specifying the minimum and maximum values(boundary) under which the solution for the `maximize` reaction should fall
`externals` | a character vector of metabolites as provided by the user for speficific pathways for which FBA (flux balance analysis needs to be performed)
`file.name` | a character string specifying the name of the LIM file created by the function.

### Value

A model file with with extension `".lim"` is created

### Note

none

### Author(s)

Anand K. Gavai <anand.gavai@bioinformatics.nl>, Hannes Hettling <j.hettling@vu.nl>

### References

Soetaert K, van Oevelen D (2009). LIM: Linear Inverse Model examples and solution methods. R package version 1.3

### Examples

    ##Create a LIM model file from a reactions file in the examples
    path <- system.file("extdata", "Glycolysis_TCA_recon1_reactionIDs.txt", package="BiGGR")
    reaction.ids <- scan(path, what=" ")
    data("H.sapiens_Recon_1")
    sbml.model <- buildSBMLFromReactionIDs(reaction.ids, H.sapiens_Recon_1)
    maximize <- c("R_ATPS4m - R_NDPK1m - R_HEX1 - R_PFK  - R_PGK + R_PYK")
    externals <- c("M_glc_DASH_D_e", "M_lac_DASH_L_e",
    		   "M_ala_DASH_L_e", "M_gln_DASH_L_c", "M_h2o_e",
    		   "M_co2_e", "M_o2_e", "M_h_e", "M_pi_c",
    		   "M_o2s_m", "M_nh4_m", "M_adp_c",
    		   "M_atp_c", "M_nadp_c", "M_nadph_c", "M_h_c")
    equation.vars <- c("R_GLCt1r", "R_O2t", "R_L_LACt2r", "R_GLNtm")
    equation.values <- c(0.4, 2.4, 0.0, 0.0)
    eqns <- list(equation.vars, equation.values)
    constraints <- list(c("R_GLCt1r", "R_CYOOm3"), c(-1000, -1000), c(1000, 1000))
    limfile.name <- tempfile()
    createLIMFromSBML(sbml.model, maximize, equations=eqns,
    			  inequalities=list("R_O2t", 2.4, "<="),
    			  constraints=constraints, externals=externals,
    			  file.name=limfile.name)

[Package BiGGR version 1.18.0 Index]