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optStoic Python tutorial

  • Author: Chiam Yu Ng
  • Reference: Chiam Yu Ng, Lin Wang, Anupam Chowdhury and Costas D. Maranas, 2018 (under review)
  • Details on the algorithms is provided in the paper.

Methods

  1. Setup your optStoic design equation.

  2. Create a user_defined_export_rxns_Sji dictionary of exchange reactions for each metabolite that participate in the equation. E.g.,

user_defined_export_rxns_Sji = {
    'EX_glc': {'C00031': -1.0},
    'EX_nad': {'C00003': -1.0},
    'EX_adp': {'C00008': -1.0},
    'EX_phosphate': {'C00009': -1.0},
    'EX_pyruvate': {'C00022': -1.0},
    'EX_nadh': {'C00004': -1.0},
    'EX_atp': {'C00002': -1.0},
    'EX_h2o': {'C00001': -1.0},
    'EX_hplus': {'C00080': -1.0},
    'EX_nadp': {'C00006': -1.0},
    'EX_nadph': {'C00005': -1.0}
    }
  1. Create a specific_bounds dictionary for the upper and lower bound to the exchange flux.
specific_bounds = {'EX_glc': {'LB': -1, 'UB': -1},
                'EX_pyruvate': {'LB': 2, 'UB': 2},
                'EX_nad': {'LB': -2, 'UB': 0},
                'EX_nadh': {'LB': 0, 'UB': 2},
                'EX_nadp': {'LB': -2, 'UB': 0},
                'EX_nadph': {'LB': 0, 'UB': 2},
                'EX_adp': {'LB': -1, 'UB': -1},
                'EX_phosphate': {'LB': -1, 'UB': -1},
                'EX_atp': {'LB': 1, 'UB': 1},
                'EX_h2o': {'LB': 1, 'UB': 1},
                'EX_hplus': {'LB': -10, 'UB': 10}}
  1. Setup your custom constraints for the pathway.
v('EX_nadph') + v('EX_nadh') = 2;
v('EX_nadp') + v('EX_nad') = -2;
v('EX_nadh') + v('EX_nad') = 0;
v('EX_nadph') + v('EX_nadp') = 0;

can be written as:

custom_flux_constraints = [
        {'constraint_name': 'nadphcons1',
         'reactions': ['EX_nadph', 'EX_nadh'],
         'UB': 2,
         'LB': 2},
        {'constraint_name': 'nadphcons2',
        'reactions': ['EX_nadp', 'EX_nad'],
        'UB': -2,
        'LB': -2},
        {'constraint_name': 'nadphcons3',
        'reactions': ['EX_nadh', 'EX_nad'],
        'UB': 0,
        'LB': 0},
        {'constraint_name': 'nadphcons4',
        'reactions': ['EX_nadph', 'EX_nadp'],
        'UB': 0,
        'LB': 0}]

  1. Perform blocked reaction analysis (see optstoicpy.script.data_preprocessing.blocked_reactions_analysis details).

  2. Perform internal loop analysis to obtain the Nint matrix (see optstoicpy.script.data_preprocessing.test_internal_loop_analysis for details).

  3. Setup optStoic database loading (optstoicpy.core.database.load_db_v3).

  4. Finally, setup the optStoic simulation (optstoicpy.script.opstoic).

  5. Visualize pathways (optstoicpy.core.drawpathway) and analyze pathways (optstoicpy.script.pathway_analysis)