get_ipython().getoutput("wget -nc http://bigg.ucsd.edu/static/models/iJO1366.json") builder.model = cobra.io.load_json_model('iJO1366.json') # Run FBA with the model and add the flux data to the map solution = builder.model.optimize() builder.reaction_data = solution.fluxes # Add some data for metabolites builder.metabolite_data = solution.shadow_prices # Simplify the map by hiding some labels builder.hide_secondary_metabolites = True builder.hide_all_labels = True builder.reaction_scale = [ { 'type': 'min', 'color': '#000000', 'size': 12 }, { 'type': 'median', 'color': '#ffffff', 'size': 20 }, { 'type': 'max', 'color': '#ff0000', 'size': 25 } ] builder.reaction_scale_preset = 'GaBuRd' # Make all the arrows three times as thick builder.reaction_scale = [