library(simmer) options(stringsAsFactors = F) ## Load files describing valid reactions, species (their composition) both from the core SBML model and supplemented manual annotations load_metabolic_model() ## Load files describing boundary conditions, reaction reversibility and auxotrophies format_boundary_conditions() ## Setup matrices defining the stoichiometry of each reaction and how reactions will be constrained ### identify reaction that cannot carry flux based on inputs, outputs and directionality infRxMet <- setup_FBA_constraints(return_infeasible = T, infRxMet = NULL) #### prune infeasible reactions and format data for optimization setup_FBA_constraints(return_infeasible = F, infRxMet) # calculate fluxes using quadratic programming inferred_fluxes <- calculate_QP_fluxes() knitr::kable(head(dplyr::select(inferred_fluxes, reactionID:`P0.30`), 5)) # generate files to read into python for calculating upper and lower bounds on flux using FVA # read_write_python_FVA(status = "write", directory = "~/Desktop/")
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