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%matplotlib inline

Mussel Physiology Model

In this tutorial, we'll play with a mussel physiology model. You may want to think about it as placing one single mussel in a large pool with water. You can change the conditions of the pool... but the mussel is so little incomparison to the pool, that it would not feedback... that is, it has no impact on the concentration of phytoplankton, oxygen, etc.

The model is based on:

Ibarra, Fennel, Cullen (2014) Coupling 3-D Eulerian bio-physics (ROMS) with individual-based shellfish ecophysiology (SHELL-E): A hybrid model for carrying capacity and environmental impacts of bivalve aquaculture. Ecological Modelling 273 (2014) 63- 78

Lets load and run our "toy" mussel model. Make sure that have in your working directory the following file: model_Mussel_IbarraEtal2014.py



In [27]:

    
import model_Mussel_IbarraEtal2014 as mymodel

# load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

You can see how our "mussel" grows and spawns 3 times in 3 years. First spawing occured at year = 2

Now lets see if we lower the Oxygen concentration of the pool.



In [28]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Oxy'] = 25. #Oxygen ...note that the default is 30

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Yikes! The mussel doesn't like the lower oxygen concentration, it grows slower, and it does not gets the chance to spawn.

Lets reset to defaults, and lets see what happens if there is "low" food in our pool...



In [29]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Phy'] = 0.5 #Phyto ...note that the default is 2

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Wow! Our mussel grew so slow that it even reach puberty

Lets run it again but with more phytoplankton



In [30]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Phy'] = 1.5 #Phyto ...note that the default is 2

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Ok. It reached puberty at 1.5 years. But it still did not spawn after 3 years!

Let's do more. Lets see if we can starve the poor mussel. Let's say no food at all!



In [31]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Phy'] = 0. #Phyto ...note that the default is 2
InitCond['Zoo'] = 0. #Zoo
InitCond['SDet'] = 0. #SDet

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Our mussel looses about 85% of its weight in 3 years. In reality, it probably would have died... but our model allows it to keep loosing weight, until each reaches biomass = zero.

One more run... lets feed our mussel like a king!



In [32]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Phy'] = 10. #Phyto ...note that the default is 2

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Now our mussel spawns about 6 times per year.

One last run... lets keep feeding our mussel like a king, but decrease the temperaure to -3.5 degrees celcius (Brrr!)



In [37]:

    
# Re-load default parameters
days, dt, par, InitCond = mymodel.load_defaults()

# Change a few things
InitCond['Temp'] = 1 #Temperature...note that the default is 10

 # run the model
output = mymodel.run_model(days,dt,InitCond,par)

# plot model
mymodel.plot_model(output)









    



Model run: DONE!!!

Mussels (Mytilus edulis) are pretty ok in cold water. As you see, they are just fine in low temperatures as long as they have food.