Codes to simulate growth under normal and stress conditions
- Install cobra version = 0.4.1, pandas version = 0.13.1 or 0.17.1, xlrd version = 0.9.0
- Cobrapy is provided with this repository (version 0.4.1) that might require manual setup. It is recommended to install through proper channel (see https://pypi.org/project/cobra/).
- Install other packages like scipy, matplotlib, libsbml, lxml etc. (see scobra documentation)
- Use the existing Scobra with this code (unzip, no installation required)
Example to obtain FBA solutions and growth curves:
#to run
In [1]: import rice_growth_model_with_WOFOST
In [2]: normal_growth = rice_growth_model_with_WOFOST.Growth() #use WOFOST_rates_one_plant.csv
In [3]: water_limited_growth = rice_growth_model_with_WOFOST.Growth() # use WOFOST_rates_one_plant_stress.csv (reload)
#to load
In [1]: import pickle
In [2]: f = open('normal.pkl','rb')
In [3]: normal_growth = pickle.load(f)
In [4]: f.close()
In [5]: f = open('stress.pkl','rb')
In [6]: water_limited_growth = pickle.load(f)
In [7]: f.close()