How to use the tellurium.sedml.utils.run_case function in tellurium

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github sys-bio / tellurium / examples / tellurium-files / phrasedml / parameterScan1D.py View on Github external
J2_q = 3;
J3_k2 = 5;

// Other declarations:
const compartment_, J0_v0, J1_k3, J2_k1, J2_k_1, J2_c, J2_q, J3_k2;
end
'''
p_str = '''
model1 = model "parameterScan1D"
timecourse1 = simulate uniform(0, 20, 1000)
task0 = run timecourse1 on model1
task1 = repeat task0 for J0_v0 in [8, 4, 0.4], reset=true
plot task1.time vs task1.S1, task1.S2
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / simpletimecourse.py View on Github external
J9_KK10 = 15;

  // Other declarations:
  const compartment_, J0_V1, J0_Ki, J0_n, J0_K1, J1_V2, J1_KK2, J2_k3, J2_KK3;
  const J3_k4, J3_KK4, J4_V5, J4_KK5, J5_V6, J5_KK6, J6_k7, J6_KK7, J7_k8;
  const J7_KK8, J8_V9, J8_KK9, J9_V10, J9_KK10;
end
'''
p_str = '''
model1 = model "MAPKcascade"
sim1 = simulate uniform(0,4000,1000)
task1 = run sim1 on model1
plot task1.time vs task1.MAPK, task1.MAPK_P, task1.MAPK_PP
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / lorenz.py View on Github external
x' = sigma*(y - x);
  y' = x*(rho - z) - y;
  z' = x*y - beta*z;
  x = 0.96259;  y = 2.07272;  z = 18.65888;
  sigma = 10;  rho = 28; beta = 2.67;
end
'''

p_str = '''
model1 = model "lorenz"
sim1 = simulate uniform(0,15,2000)
task1 = run sim1 on model1
plot task1.z vs task1.x
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_11.py View on Github external
S1 = 10.0; S2 = 0.0;
  k1 = 0.5; k2=0.4
end
'''
p_str = '''
  mod1 = model "case_11"
  sim1 = simulate uniform(0, 10, 100)
  task1 = run sim1 on mod1
  rtask1 = repeat task1 for k1 in uniform(0, 1, 2)
  rtask2 = repeat rtask1 for k2 in uniform(0, 1, 3)
  rtask3 = repeat rtask2 for S1 in [5, 10], reset=true
  plot "RepeatedTask of RepeatedTask" rtask3.time vs rtask3.S1, rtask3.S2
  plot rtask3.k1 vs rtask3.k2 vs rtask3.S1
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_04.py View on Github external
k1 = 0.5; k2=0.4
end
'''
p_str = '''
  mod1 = model "case_04"
  mod2 = model mod1 with S2=S1+4
  mod3 = model mod2 with S1=20.0
  sim1 = simulate uniform(0, 10, 100)
  task1 = run sim1 on mod1
  task2 = run sim1 on mod2
  task3 = run sim1 on mod3
  plot "Example plot" task1.time vs task1.S1, task1.S2, task2.S1, task2.S2, task3.S1, task3.S2
  report task1.time vs task1.S1, task1.S2, task2.S1, task2.S2, task3.S1, task3.S2
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / parameterScan2D.py View on Github external
const J3_k4, J3_KK4, J4_V5, J4_KK5, J5_V6, J5_KK6, J6_k7, J6_KK7, J7_k8;
  const J7_KK8, J8_V9, J8_KK9, J9_V10, J9_KK10;
end
'''

p_str = '''
  model_3 = model "parameterScan2D"
  sim_repeat = simulate uniform(0,3000,100)
  task_1 = run sim_repeat on model_3
  repeatedtask_1 = repeat task_1 for J1_KK2 in [1, 5, 10, 50, 60, 70, 80, 90, 100], reset=true
  repeatedtask_2 = repeat repeatedtask_1 for J4_KK5 in uniform(1, 40, 10), reset=true
  plot repeatedtask_2.J4_KK5 vs repeatedtask_2.J1_KK2
  plot repeatedtask_2.time vs repeatedtask_2.MKK, repeatedtask_2.MKK_P
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_09.py View on Github external
const J3_k4, J3_KK4, J4_V5, J4_KK5, J5_V6, J5_KK6, J6_k7, J6_KK7, J7_k8;
const J7_KK8, J8_V9, J8_KK9, J9_V10, J9_KK10;
end
'''

p_str = '''
  mod1 = model "case_09"
  # sim1 = simulate uniform_stochastic(0, 4000, 1000)
  sim1 = simulate uniform(0, 4000, 1000)
  task1 = run sim1 on mod1
  repeat1 = repeat task1 for local.x in uniform(0, 10, 10), reset=true
  plot "MAPK oscillations" repeat1.MAPK vs repeat1.time vs repeat1.MAPK_P, repeat1.MAPK vs repeat1.time vs repeat1.MAPK_PP, repeat1.MAPK vs repeat1.time vs repeat1.MKK
  report repeat1.MAPK vs repeat1.time vs repeat1.MAPK_P, repeat1.MAPK vs repeat1.time vs repeat1.MAPK_PP, repeat1.MAPK vs repeat1.time vs repeat1.MKK
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_10.py View on Github external
k1 = 0.5; k2=0.4
end
'''

p_str = '''
  mod1 = model "case_10"
  mod2 = model "case_10"
  sim1 = simulate uniform(0, 10, 100)
  sim2 = simulate uniform(0, 3, 10)
  task1 = run sim1 on mod1
  task2 = run sim2 on mod2
  repeat1 = repeat [task1, task2] for local.X in uniform(0, 10, 9), mod1.S1 = X, mod2.S1 = X+3
  plot repeat1.mod1.time vs repeat1.mod1.S1, repeat1.mod1.S2, repeat1.mod2.time vs repeat1.mod2.S1, repeat1.mod2.S2
'''

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_02.py View on Github external
end
"""

p_str = """
    model0 = model "case_02"
    model1 = model model0 with S1=5.0
    sim0 = simulate uniform(0, 6, 100)
    task0 = run sim0 on model1
    task1 = repeat task0 for k1 in uniform(0.0, 5.0, 5), reset = true
    plot "Repeated task with reset" task1.time vs task1.S1, task1.S2
    report task1.time vs task1.S1, task1.S2
    plot "Repeated task varying k1" task1.k1 vs task1.S1
    report task1.k1 vs task1.S1
"""

run_case(os.path.realpath(__file__), a_str, p_str)
github sys-bio / tellurium / examples / tellurium-files / phrasedml / case_12.py View on Github external
end
'''

p_str = '''
  mod1 = model "case_12"
  sim1 = simulate uniform(0, 2, 10, 49)
  sim2 = simulate uniform(0, 15, 49)
  task1 = run sim1 on mod1
  task2 = run sim2 on mod1
  repeat1 = repeat task1 for S1 in uniform(0, 10, 4), S2 = S1+20, reset=true
  repeat2 = repeat task2 for S1 in uniform(0, 10, 4), S2 = S1+20, reset=true
  plot "Offset simulation" repeat2.time vs repeat2.S1, repeat2.S2, repeat1.time vs repeat1.S1, repeat1.S2
  report repeat2.time vs repeat2.S1, repeat2.S2, repeat1.time vs repeat1.S1, repeat1.S2
'''

run_case(os.path.realpath(__file__), a_str, p_str)