InitialAssignments

Testing initial assignments



In [1]:

    
%matplotlib inline
from __future__ import print_function, division
import tellurium as te
import roadrunner
from roadrunner import SelectionRecord
from matplotlib import pyplot as plt



In [2]:

    
# load model
import Cell
r = te.loads('results/{}_{}.xml'.format(Cell.mid, Cell.version))
print(r.getCurrentAntimony())









    



// Created by libAntimony v2.9.0
model *AssignmentTest_1()

  // Assignment Rules:
  Cve := Ave/Vve;
  Vve := BW*FVve;

  // Rate Rules:
  Ave' = -k1*Cve;

  // Variable initializations:
  IVDOSE = 0;
  IVDOSE has mg;
  D = PODOSE;
  D has mg;
  PODOSE = 100;
  PODOSE has mg;
  FVve = 0.0514;
  FVve has litre_per_kg;
  k1 = 0.1;
  k1 has litre_per_h;
  BW = 70;
  BW has kg;
  Ave = IVDOSE;
  Ave has mg;
  Cve has mg_per_litre;
  Vve has litre;

  // Other declarations:
  var D, Ave, Cve, Vve;
  const IVDOSE, PODOSE, FVve, k1, BW;

  // Unit definitions:
  unit mulitre_per_g = 1e-6 litre / gram;
  unit mg = 1e-3 gram;
  unit kg = 1e3 gram;
  unit s_per_h = second / 3600 second;
  unit mg_per_g = 1e-3 gram / gram;
  unit mg_per_h = 1e-3 gram / 3600 second;
  unit ml_per_litre = 1e-3 litre / litre;
  unit m = metre;
  unit litre_per_kg = litre / 1e3 gram;
  unit h = 3600 second;
  unit mulitre_per_min_mg = 1e-6 litre / (60 second * 1e-3 gram);
  unit min_per_h = 60 second / 3600 second;
  unit litre_per_h = litre / 3600 second;
  unit m2 = metre^2;
  unit ml_per_s = 1e-3 litre / second;
  unit mg_per_litre = 1e-3 gram / litre;
  unit per_h = 1 / 3600 second;
  unit length = m;
  unit area = m2;
  unit volume = litre;
  unit substance = mg;
  unit extent = mg;
  unit time_unit = h;
end

Changing the dose

Running simulations with changing dose



In [3]:

    
for dose in [0, 10, 20, 30]:
    r.setValue('init(IVDOSE)', dose)  # oral dose in [mg]
    r.resetAll()
    print(r.Ave)

    s = r.simulate(0,24,1001)
    plt.plot(s['time'], s['Ave'], color='black')
plt.xlabel('time')
plt.ylabel('amount [mg]')
plt.show()

Testing the reset stack

r.resetToOrigin()

full reset of model to original state
resetToOrigin resets initial values (and everything else) from the originally loaded model.

r.reset()

reset just loads the initial values
values of species are now initial values

r.resetAll()

resetAll() loads the species with the current set of initial values (and resets parameters to their original loaded values



In [23]:

    
from __future__ import print_function, division

import tellurium as te 
import roadrunner 

r = te.loada(""" 
    species S1, S2, S3
    
    J1:S1 -> S2; k1*S1; 
    S1 = 1; k1 = 0.1; 
    
    // S2 via initial assignment
    S2 = S1 + 10
    
    // S3 via rule
    S3 := S1/2
    
    // p1 via initial assignment
    p1 = 10
    // p2 via rule
    p2 := p1/2
""") 
r.timeCourseSelections = r.getFloatingSpeciesIds() + r.getGlobalParameterIds()

def print_values(r, msg):
    print('***', msg, '***')
    print('<initial values>')
    for sid in r.getFloatingSpeciesIds():
        print("\t{sid} = {value}".format(sid=sid, value=r['init({})'.format(sid)]))
    print('<values>')
    for sid in r.getFloatingSpeciesIds() + r.getGlobalParameterIds():
        print("\t{sid} = {value}".format(sid=sid, value=r['{}'.format(sid)]))
    print('\n')

# plot the initial values of models
print_values(r, "Initial values")

# make a change to S1 and p1
r.S1 = 99 
r.p1 = 99
print_values(r, "Change S1 and p1")
# -> S3 and p2 are  updated also via rule

# reset() after change
r.reset()
print_values(r, "reset() after changes")
# -> S1 is reset to intial value (S3 via rule)
# -> parameters are not effected

r.resetToOrigin()
print_values(r, "resetToOrigin()")


# make a change to init(S1) and init(p1)
r['init(S1)'] = 99 
r['init(p1)'] = 99
print_values(r, "Change init(S1) and init(p1)")
# -> the values of species are updated immediatly, 
# -> ! the dependencies of the parameters are not !!!

# resetAll() after  init change
r.resetAll()
print_values(r, "resetAll() to apply changes from changed initial conditions")
# -> the values of the parameters are updated in the model from the init(p1) values

r.resetToOrigin()
print_values(r, "resetToOrigin()")

# This is not possible (the init(p1) is set, but cannot be plotted)
print('init(p1) = ', r['init(p1)'])









    



*** Initial values ***
<initial values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
<values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
	k1 = 0.1
	p1 = 10.0
	p2 = 5.0


*** Change S1 and p1 ***
<initial values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
<values>
	S1 = 99.0
	S2 = 11.0
	S3 = 49.5
	k1 = 0.1
	p1 = 99.0
	p2 = 49.5


*** reset() after changes ***
<initial values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
<values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
	k1 = 0.1
	p1 = 99.0
	p2 = 49.5


*** resetToOrigin() ***
<initial values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
<values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
	k1 = 0.1
	p1 = 10.0
	p2 = 5.0


*** Change init(S1) and init(p1) ***
<initial values>
	S1 = 99.0
	S2 = 109.0
	S3 = 49.5
<values>
	S1 = 99.0
	S2 = 109.0
	S3 = 49.5
	k1 = 0.1
	p1 = 10.0
	p2 = 5.0


*** resetAll() to apply changes from changed initial conditions ***
<initial values>
	S1 = 99.0
	S2 = 109.0
	S3 = 49.5
<values>
	S1 = 99.0
	S2 = 109.0
	S3 = 49.5
	k1 = 0.1
	p1 = 99.0
	p2 = 49.5


*** resetToOrigin() ***
<initial values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
<values>
	S1 = 1.0
	S2 = 11.0
	S3 = 0.5
	k1 = 0.1
	p1 = 10.0
	p2 = 5.0








    



---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-23-1b98bcf7f418> in <module>()
     68 
     69 # This is not possible (the init(p1) is set, but cannot be plotted)
---> 70 print('init(p1) = ', r['init(p1)'])

/usr/local/lib/python2.7/dist-packages/roadrunner/roadrunner.pyc in __getitem__(self, *args)
   2546         return _roadrunner.RoadRunner_getValue(self, *args)
   2547 
-> 2548     def __getitem__(self, *args): return _roadrunner.RoadRunner___getitem__(self, *args)
   2549     def __setitem__(self, *args): return _roadrunner.RoadRunner___setitem__(self, *args)
   2550     def getIds(self, *args):

RuntimeError: Invalid id 'p1' for floating initial amount



In [24]:

    
r.getValue('init(p1)')









    



---------------------------------------------------------------------------
RuntimeError                              Traceback (most recent call last)
<ipython-input-24-52fc8a8c989b> in <module>()
----> 1 r.getValue('init(p1)')

/usr/local/lib/python2.7/dist-packages/roadrunner/roadrunner.pyc in getValue(self, *args)
   2544 
   2545         """
-> 2546         return _roadrunner.RoadRunner_getValue(self, *args)
   2547 
   2548     def __getitem__(self, *args): return _roadrunner.RoadRunner___getitem__(self, *args)

RuntimeError: Invalid id 'p1' for floating initial amount



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