es_sample_model

PURPOSE

SYNOPSIS

DESCRIPTION

 ES_SAMPLE_MODEL - Sample all model parameters for a network

 result = es_sample_model(N, W, ind_ext, es_constraints, es_options)
 
 This script reconstructs one model instance, including the sampled elasticities.
 For samplig multiple model instances, see 'es_sample_multiple'.


 Inputs (with nm: # metabolites; nr: # reactions)
   N         - Stoichiometric matrix (nm x nr)
   W         - Allosteric regulation matrix (nr x nm)
   ind_ext   - indices of external metabolites

   For the inputs 'es_constraints' and 'es_options', see 'es_default_options'


 Outputs
   All output data are stored in a data structure 'result' (see 'es_sample_elasticities')
   es_options and es_constraints are returned with the (possible) changes made.


 Sampling consists of two stages:
   1. Steady state          (calling 'es_sample_steady_state')
   2. Elasticities and MCA  (calling 'es_sample_elasticities')

CROSS-REFERENCE INFORMATION

• es_sample_elasticities ES_SAMPLE_ELASTICITIES - Elasticity phase
• es_sample_steady_state ES_SAMPLE_STEADY_STATE - Sample feasible stationary state for a network

• es_figure_4_hepatonet_utp_paradoxical Hepatonet elasticity sampling // analysis for UTP rephosphorylation
• es_figure_5_synergies Run elasticity sampling and analyse synergies
• demo_e_coli_glycolysis demo_e_coli_glycolysis - Demo script for thermodynamically feasible elasticity sampling
• elasticity_sampling_workflow elasticity_sampling_workflow - Demo script
• elasticity_sampling_sample_prior result = elasticity_sampling_sample_prior(p)
• energetics_control_and_noise ENERGETICS_CONTROL_AND_NOISE - Analyse control coefficients and noise levels (assuming uniform white noise in each reaction!)
• es_discover_perturbation_sample ES_DISCOVER_PERTURBATION_SAMPLE
• es_simulate_perturbation_sample ES_SIMULATE_PERTURBATION_SAMPLE Predict the effects of a given differential profile
• es_reference_state ES_REFERENCE_STATE - Elasticity sampling
• es_sbml_to_model ES_SBML_TO_MODEL Wrapper function around es_sample_model
• interaction_statistics INTERACTION_STATISTICS - Run elasticity sampling repeatedly and compute statistics over the influence values
• es_sample_multiple ES_SAMPLE_MULTIPLE - Create model ensemble and collect values for an output function