3. Pseudocode

The following section includes pseudocode of some of the main operations performed by findCPcli.

• Find chokepoints on a model

function find_chokepoints(model)
    chokepoint_list = empty list
    for reaction in model
        if reaction upper flux bound not equal 0 and lower flux bound not equal 0
            for reactant in reaction
                if reaction is the only consumer of reactant
                    chokepoint_list = chokepoint_list + (reaction, reactant)
            for product in reaction
                if reaction is the only producer of product
                    chokepoint_list = chokepoint_list + (reaction, product)
    return chokepoint_list

• Find dead-end metabolites on a model

function find_dead_end_metabolites(model)
  dem_list = empty list
  for metabolite in model
      if length(metabolite.consumers) == 0 or length(metabolite.producers) == 0
          dem_list = dem_list + metabolite
  return dem_list

• Remove dead-end metabolites on a model

function remove_dead_end_metabolites(model)
    while number of metabolites in model does not change:
        find_dead_end_metabolites(model)
        delete all dead-end metabolites in model
        for reaction that produced or consumed dead-end metabolites:
            if reaction produces or consumes 0 metabolites [and is not exchange nor demand]:
                delete reaction on model
        find_dead_end_metabolites(model)
    return model

• Update model flux bounds with Flux Variability Analysis

function update_flux_bounds_with_fva(model, fraction_of_optmimum_growth)
    max_fva, min_fva = flux_variability_analysis(model, fraction_of_optmimum_growth)
    for reaction in model
        reaction.upper_flux_bound = max_fva[reaction]
        reaction.lower_flux_bound = min_fva[reaction]
    return model

• Find essential reactions

function find_essential_reactions(model)
  essential_reactions = empty list
  for reaction in model
      knock out reaction
      if flux_balance_analysis on model is 0
          essential_reactions = essential_reactions + reaction
      undo knock out
  return essential_reactions