print(yeast_model.optimize()) print(maritima_model.optimize()) print("--------------------------------------------------------------") print("Finding transport reactions") yeast_transport_reactions = get_transport_reaction_list(yeast_model) maritima_transport_reactions = get_transport_reaction_list(maritima_model) print("--------------------------------------------------------------") print("Finding exchange reactions") yeast_exchange_reactions = get_exchange_reaction_list(yeast_model) maritima_exchange_reactions = get_exchange_reaction_list(maritima_model) print("--------------------------------------------------------------") print("Stitching models") stitched_model = stitch_models(yeast_model,maritima_model) print("--------------------------------------------------------------") print("Performing FBA with a range of biomass ratios") number_of_objective_ratios = 20 fig = plt.figure() stitched_model.reactions.get_by_id('ETOHt_mod1').lower_bound = -10000 stitched_model.reactions.get_by_id('ETOHt_mod1').upper_bound = 10000 biomass_dataframe = simulate_variable_abundance(stitched_model,number_of_objective_ratios) ax1 = fig.add_subplot(1,5,1) biomass_dataframe.plot(kind='area',stacked=True,ax=ax1,sharey=True,\ y=['Yeast biomass','Thermotoga biomass']) ax1.xaxis.set_visible(False) stitched_model.reactions.get_by_id('ETOHt_mod1').upper_bound = 0 biomass_dataframe = simulate_variable_abundance(stitched_model,number_of_objective_ratios)
# community_phase_plane.py import os import cobra from cobra.flux_analysis import calculate_phenotype_phase_plane import model_stitcher import matplotlib.pyplot as plt if __name__ == "__main__": os.chdir("../models") yeast_file = "iMM904.xml" maritima_file = "iLJ478.xml" yeast_path = "/".join([os.getcwd(), yeast_file]) maritima_path = "/".join([os.getcwd(), maritima_file]) yeast_model = cobra.io.sbml3.read_sbml_model(yeast_path) maritima_model = cobra.io.sbml3.read_sbml_model(maritima_path) os.chdir("..") stitched_model = model_stitcher.stitch_models(yeast_model, maritima_model) data = calculate_phenotype_phase_plane(yeast_model, "EX_glc__D_e", "EX_o2_e") print data fig = plt.figure() ax = data.plot_matplotlib() plt.show() else: print "loading community_phase_plane.py"