diff --git a/docs/src/examples/07a-srba.jl b/docs/src/examples/07a-srba.jl index 1506a0fd..9762d45e 100644 --- a/docs/src/examples/07a-srba.jl +++ b/docs/src/examples/07a-srba.jl @@ -248,6 +248,8 @@ function with_srba_constraints(ct, mu; ribosome_aa_per_second = 12) ), ) #+ + # Add the ribosome mass into the total capacity bound + rbatree.gene_product_capacity.total.value += rbatree.total_ribosome_mass.value return rbatree end @@ -256,14 +258,13 @@ end # Here we use screen to efficiently run all the simulations through the # expectably viable growth range -mus = range(0.1, 1.0, 10) # simulate at these growth rates +mus = range(0.1, 1.2, 10) # simulate at these growth rates @time res = screen(mus, workers = [1]) do mu rba_constraints = with_srba_constraints(ct, mu, ribosome_aa_per_second = 12) sol = optimized_values( rba_constraints; - objective = rba_constraints.gene_product_capacity.total.value + - rba_constraints.total_ribosome_mass.value, + objective = rba_constraints.gene_product_capacity.total.value, sense = Minimal, optimizer = HiGHS.Optimizer, ) @@ -272,7 +273,7 @@ mus = range(0.1, 1.0, 10) # simulate at these growth rates mu, membrane_mass = sol.gene_product_capacity.membrane, ribosome_mass = sol.total_ribosome_mass, - enzyme_mass = sol.total_enzyme_mass, + enzyme_mass = sol.gene_product_capacity.total - sol.total_ribosome_mass, total_mass = sol.gene_product_capacity.total, ac_flux = sol.fluxes.EX_ac_e, glc_flux = sol.fluxes.EX_glc__D_e,