GSMM_Simulations.ipynb

 
 
Calculations of Substrate and Production Rates and Yields

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 import os
import pandas as pd
# import numpy as np
from datetime import date

import matplotlib.pyplot as plt
%matplotlib inline

from cobra.io import read_sbml_model, write_sbml_model
from iambcodes.cobra import *
 
 Data loading and variables setup
 Today = date.today().strftime('%y%m%d')
BaseDir = '/home/ulf/Documents/Ustilago_maydis-GEM/'
TargetDir = os.path.join(BaseDir, 'data/Simulations')
ImageType = 'png'
SBMLFile = 'iCL1079.xml'
SBMLAddress = os.path.join(BaseDir, 'model', SBMLFile)

model = read_sbml_model(SBMLAddress)
model
 
 Substrate tests
In the following code, the model is tested for growth rates on defined substrates and the corresponding uptake rates.
 SubNames = ['EX_glc__D_e','EX_glc__D_e','EX_glc__D_e']
SubRates = [.1, 1, 1.5]

Growth = list()
for myName, myRate in zip(SubNames, SubRates):
    Growth.append(TestSubstrate(model, EX_Sub_Act=[myName], EX_Sub_Off=['EX_glc__D_e'], Rate=myRate))
    
plt.plot(SubRates, Growth, 'o')
 
 Plotting simulation and measured growth
 RCFile = os.path.join(BaseDir,'data','GrowthRates','RatesCompare.xlsx')
RCSheet = 'RateCompare'
FigureGrowth = '{}_Growth_SimVsExp.{}'.format(Today, ImageType)
FigureGrowthPath = os.path.join(TargetDir, FigureGrowth)

RateComp = pd.read_excel(RCFile, sheet_name=RCSheet)
# Substrate acceleration plot
plt.errorbar(RateComp['Substrate-uptake'], RateComp['Growth-Rate'], xerr=RateComp['Uptake-Std'], yerr=RateComp['Growth-Rate-Std'], fmt='ok', label='exp. growth rates') #, 'xk', label='Substrate uptake'
# plt.plot(RateComp['Growth-Rate'], SA_ic+SubAcc*RateComp['Growth-Rate'], '-k', label='fit, accel.{}(+/-{})mmol/gCDW/h/h'.format(round(SubAcc,2), round(SA_sl_sterr,2)))
plt.title('Growth rate VS substrate uptake')
plt.xlabel('Substrate uptake in mmol/gCDW/h')
plt.ylabel('Growth rate in /h')
plt.plot(SubRates, Growth, 'xr', label='simulations', ms=10, markeredgewidth=3)
plt.legend()
plt.savefig(FigureGrowthPath)
plt.show()
print('Growth rate versus substrate uptake figure saved as {}'.format(FigureGrowthPath))