ES_DEFAULT_OPTIONS - Set default values in 'es_options' and 'es_constraints'
[es_options, es_constraints] = es_default_options(N)
Initialise structures 'es_options' and 'es_constraints'
used to define tasks in elasticity sampling
N is either the (complete) stoichiometric matrix
or a network data structure from the Metabolic Network Toolbox)
1. The structure es_constraints contains information for defining
the constraints in model sampling
Field name Size Meaning
---------- ---- -------
es_constraints.v_fix nr x 1 fluxes predefined values (overrides vmin and vmax)
es_constraints.v_min nr x 1 fluxes lower bounds (overrides -vmax)
es_constraints.v_max nr x 1 fluxes upper bounds
es_constraints.v_sign nr x 1 fluxes signs (overrides vmin and vmax)
es_constraints.v_mean nr x 1 fluxes data (can also be a matrix)
es_constraints.v_std nr x 1 fluxes data error bars (can also be a matrix)
es_constraints.Keq_fix nr x 1 equilibrium constants predefined values
es_constraints.ext_sign nx x 1 signs of production rates of external metabolites
es_constraints.log_c_fix nm x 1 ln metabolite levels predefined values
es_constraints.log_c_min nm x 1 ln metabolite levels lower bounds
es_constraints.log_c_max nm x 1 ln metabolite levels upper bounds
es_constraints.log_c_mean nm x 1 ln metabolite levels data
es_constraints.log_c0_mean nm x 1 ln equilibrium metabolite levels data
es_constraints.log_c0_std nm x 1 ln equilibrium metabolite levels data error bars
es_constraints.mu0_fix nm x 1 std chemical potentials predefined values
es_constraints.mu0_min nm x 1 std chemical potentials lower bounds
es_constraints.mu0_max nm x 1 std chemical potentials upper bounds
es_constraints.mu_fix nm x 1 chemical potentials predefined values
es_constraints.mu_min nm x 1 chemical potentials lower bounds
es_constraints.mu_max nm x 1 chemical potentials upper bounds
es_constraints.dmu_fix nr x 1 Reaction Gibbs free energies predefined values
es_constraints.dmu_min nr x 1 Reaction Gibbs free energies lower bounds
es_constraints.dmu_max nr x 1 Reaction Gibbs free energies upper bounds
es_constraints.dmu_limit 1 x 1 Reaction Gibbs free energies upper limit for absolute values
es_constraints.dmu_limit_min 1 x 1 Reaction Gibbs free energies lower limit for absolute values
es_constraints.log_u_mean nr x 1 ln enzyme levels data
es_constraints.log_u_std nr x 1 ln enzyme levels data error bars
es_constraints.beta_M_fix nr x nm saturation values beta_M predefined values
es_constraints.beta_A_fix nr x nm saturation values beta_A predefined values
es_constraints.beta_I_fix nr x nm saturation values beta_I predefined values
es_constraints.alpha_A_mean nr x nm mean values for alpha_A (only for beta distribution)
es_constraints.alpha_A_std nr x nm std dev values for alpha_A (only for beta distribution)
es_constraints.alpha_I_mean nr x nm mean values for alpha_I (only for beta distribution)
es_constraints.alpha_I_std nr x nm std dev values for alpha_I (only for beta distribution)
es_constraints.alpha_M_mean nr x nm mean values for alpha_M (only for beta distribution)
es_constraints.alpha_M_std nr x nm std dev values for alpha_M (only for beta distribution)
es_constraints.rho 1 x 1 upper bound on v+/v or v-/v
es_constraints.dmu_eqconstraint struct Fields .matrix, .vector define equality constraints
es_constraints.mu_eqconstraint struct Fields .matrix, .vector define equality constraints
with nr = #reactions; nm = #metabolites; nx = #external metabolites
For defining only some entries in a vector, replace the others by 'nan'
2. The structure es_options contains general directives for the algorithm
Name Type/default Meaning
---- ------------ -------
es_options.seed Random seed
es_options.sampling_method Strategy for steady state sampling
'v from data'
'v and mu'
'c0 and c'
es_options.method_flux_sampling Strategy for flux sampling
'sample_and_discard'
'convex_optimisation'
'cycle_correction'
es_options.n_flux_samples 1 Number of flux samples
es_options.flux_units 'dimensionless', 'mM/s', 'mol/s'
es_options.n_samples 1 Number of samples in multiple sampling (model ensemble)
es_options.n_dmu_samples 1 For each of these: number of reaction affinity samples
es_options.n_saturation_samples 1 For each of these: number of elasticity samples
es_options.kinetic_law string Type of modular rate law (see modular rate laws, e.g., 'cs', 'ms')
es_options.h nr x 1 Predefined reaction cooperativities
es_options.set_alpha_to_half boolean Set all saturation values to 0.5 instead of random sampling?
es_options.set_alpha_nonuniform boolean Draw alpha values from beta distribution?
Use distribution parameters from the sparse matrices
es_constraints.alpha_A_mean etc (only nonzero entries are used):
es_options.KV_prior_mean = 1; kV value to be substituted in inactive reactions
es_options.limit_cooperativity = 2; threshold value for reaction cooperativity
es_options.no_equilibrium boolean If rates vanish, assume that zero enzyme levels are the reason
es_options.ind_ignore [] Indices of reactions to be ignored when computing thermodynamic
loops (only in for flux correction by loop substraction)
es_options.zc [] Metabolite derivative of objective function
es_options.zv [] Flux derivative of objective function
es_options.verbose (boolean) Verbose output?
es_options.graphics_flag (boolean) Show graphics?
es_options.print_graphics (boolean) Save graphics to file?