createLIMFromSBML: Create a LIM model object from an SBML file

In hettling/BiGGR: Constraint based modeling in R using metabolic reconstruction databases

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 <[e-mail]>, Hannes Hettling <[e-mail]>

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)

hettling/BiGGR documentation built on April 17, 2020, 5:19 a.m.