Add thirty models

.github/workflows/pytest.yml

@@ -23,6 +23,7 @@ jobs:
         python-version: ${{ matrix.python-version }}
     - name: Install dependencies
       run: |
+        sudo apt-get install libsundials-dev -y
         python -m pip install --upgrade pip
         python -m pip install .[test]
     - name: Lint with flake8

markov_builder/example_models.py

@@ -49,7 +49,7 @@ def construct_four_state_chain():
                        'k_3': positive_rate_expr + ((0.0873, 8.91E-3),),
                        'k_4': negative_rate_expr + ((5.15E-3, 0.003158),)}
 
-    mc.parameterise_rates(rate_dictionary, shared_variables=('V',))
+    mc.parameterise_rates(rate_dictionary)
 
     open_state = mc.get_state_symbol('O')
     auxiliary_expression = sp.sympify(f"g_Kr * {open_state} * (V - E_Kr)")
@@ -115,7 +115,7 @@ def construct_wang_chain():
                        'b_1': negative_rate_expr + ((0.006497, 0.03268),)
                        }
 
-    mc.parameterise_rates(rate_dictionary, shared_variables=('V',))
+    mc.parameterise_rates(rate_dictionary)
 
     open_state = mc.get_state_symbol('O')
 
@@ -217,7 +217,7 @@ def construct_kemp_model():
         'b_h': positive_rate_expr + ((2.70e-01, 1.58e-02),),
     }
 
-    mc.parameterise_rates(rate_dictionary, shared_variables=('V',))
+    mc.parameterise_rates(rate_dictionary)
 
     open_state = mc.get_state_symbol('O')
 

markov_builder/models/thirty_models/__init__.py

@@ -0,0 +1,15 @@
+from .model0 import model_00
+from .model1 import model_01
+from .model2 import model_02
+from .model3 import model_03
+from .model4 import model_04
+from .model5 import model_05
+from .model6 import model_06
+from .model7 import model_07
+from .model8 import model_08
+from .model11 import model_11
+from .model30 import model_30
+
+
+__all__ = ['model_00', 'model_01', 'model_02', 'model_03', 'model_04',
+           'model_05', 'model_06', 'model_07', 'model_08', 'model_11', 'model_30']

markov_builder/models/thirty_models/model0.py

@@ -0,0 +1,37 @@
+import numpy as np
+
+from markov_builder import MarkovChain
+from markov_builder.rate_expressions import negative_rate_expr, positive_rate_expr
+
+
+class model_00(MarkovChain):
+    description = ""
+    states = ('O', 'C', 'I', 'IC')
+    rates = [('O', 'C', 'k_2', 'k_1'),
+             ('I', 'IC', 'k_2', 'k_1'),
+             ('O', 'I', 'k_3', 'k_4'),
+             ('C', 'IC', 'k_3', 'k_4')]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': np.NaN}
+
+    rate_dictionary = {'k_1': positive_rate_expr + ((2.26E-4, 6.99E-2),),
+                       'k_2': negative_rate_expr + ((3.45E-5, 5.460E-2),),
+                       'k_3': positive_rate_expr + ((0.0873, 8.91E-3),),
+                       'k_4': negative_rate_expr + ((5.15E-3, 0.03158),)}
+    auxiliary_expression = "g_Kr * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'g_Kr': 0.1524,
+                             'E_Kr': -88
+                             }
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)

markov_builder/models/thirty_models/model1.py

@@ -0,0 +1,32 @@
+from numpy import NaN
+
+from markov_builder.MarkovChain import MarkovChain
+from markov_builder.rate_expressions import negative_rate_expr, positive_rate_expr
+
+
+class model_01(MarkovChain):
+    description = ""
+    states = ('O', 'C')
+    rates = [('O', 'C', 'k_21', 'k_12')]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': NaN}
+    rate_dictionary = {'k_12': positive_rate_expr + ((2.26E-4, 6.99E-2),),
+                       'k_21': negative_rate_expr + ((3.45e-5, 0.05462),)}
+
+    auxiliary_expression = "g_Kr * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'g_Kr': 0.1524,
+                             'E_Kr': -88
+                             }
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)

markov_builder/models/thirty_models/model11.py

@@ -0,0 +1,66 @@
+from numpy import NaN
+
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_11(MarkovChain):
+    description = ""
+    states = ('O', 'I', 'IC1', 'IC2', 'C2', 'C1')
+    rates = [
+        ('O', 'I', 'ah', 'bh'),
+        ('C1', 'O', 'a1', 'b1'),
+        ('IC1', 'I', 'a3', 'b3'),
+        ('IC2', 'IC1', 'a4', 'b4'),
+        ('C2', 'C1', 'a2', 'b2'),
+        ('C2', 'IC2', 'ah', 'bh'),
+        ('C1', 'IC1', 'ah', 'bh')
+    ]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': NaN,
+                             'p1': 2.26e-4,
+                             'p2': 0.06990,
+                             'p3': 3.45e-5,
+                             'p4': 0.05462,
+                             'p5': 0.08730,
+                             'p6': 8.91e-3,
+                             'p7': 5.15e-3,
+                             'p8': 0.03158,
+                             'p9': 2.26e-4,
+                             'p10': 0.06990,
+                             'p11': 3.45e-5,
+                             'p12': 0.05462,
+                             'p13': 0.08730,
+                             'p14': 8.91e-3,
+                             'p15': 5.15e-3,
+                             'p16': 0.03158,
+                             'p17': 0.15240
+                             }
+
+    rate_dictionary = {
+        'a1': ('p1 * exp( p2 * V)',),
+        'b1': ('p3 * exp(-p4 * V)',),
+        'ah': ('p5 * exp( p6 * V)',),
+        'bh': ('p7 * exp(-p8 * V)',),
+        'a2': ('p9 * exp( p10 * V)',),
+        'b2': ('p11 * exp(-p12 * V)',),
+        'a3': ('p13 * exp( p14 * V)',),
+        'b3': ('(a3*b1)/a1',),
+        'a4': ('p15 * exp(p16* V)',),
+        'b4': ('(a4*b2)/a2',)
+    }
+
+    auxiliary_expression = "p17 * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'E_Kr': -85}
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)

markov_builder/models/thirty_models/model2.py

@@ -0,0 +1,36 @@
+from numpy import NaN
+
+from markov_builder.MarkovChain import MarkovChain
+from markov_builder.rate_expressions import negative_rate_expr, positive_rate_expr
+
+
+class model_02(MarkovChain):
+    description = ""
+    states = ('O', 'C', 'I')
+    rates = [('O', 'C', 'bm', 'am'),
+             ('O', 'I', 'ah', 'bh')]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': NaN}
+    rate_dictionary = {'am': positive_rate_expr + ((2.26E-4, 6.99E-2),),
+                       'bm': negative_rate_expr + ((3.45E-5, 5.462E-2),),
+                       'ah': positive_rate_expr + ((0.08730, 8.91e-3),),
+                       'bh': negative_rate_expr + ((5.15e-3, 0.03158),),
+                       }
+
+    auxiliary_expression = "g_Kr * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'g_Kr': 0.1524,
+                             'E_Kr': -88
+                             }
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)

markov_builder/models/thirty_models/model3.py

@@ -0,0 +1,38 @@
+from numpy import NaN
+
+from markov_builder.MarkovChain import MarkovChain
+from markov_builder.rate_expressions import negative_rate_expr, positive_rate_expr
+
+
+class model_03(MarkovChain):
+    description = ""
+    states = ('O', 'C', 'I', 'IC')
+    rates = [('O', 'C', 'bm', 'am'),
+             ('I', 'IC', 'bm', 'am'),
+             ('O', 'I', 'ah', 'bh'),
+             ('C', 'IC', 'ah', 'bh')]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': NaN}
+    rate_dictionary = {'am': positive_rate_expr + ((2.26E-4, 6.99E-2),),
+                       'bm': negative_rate_expr + ((3.45E-5, 5.462E-2),),
+                       'ah': positive_rate_expr + ((0.08730, 8.91e-3),),
+                       'bh': negative_rate_expr + ((5.15e-3, 0.03158),),
+                       }
+
+    auxiliary_expression = "g_Kr * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'g_Kr': 0.1524,
+                             'E_Kr': -88
+                             }
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)

markov_builder/models/thirty_models/model30.py

@@ -0,0 +1,116 @@
+from numpy import NaN
+
+from markov_builder.MarkovChain import MarkovChain
+
+
+class model_30(MarkovChain):
+    description = ""
+    states = ('O', 'I', 'IC1', 'IC2', 'C2', 'C1', 'C3', 'IC3', 'IC4', 'C4')
+    rates = [
+        ('C1', 'O', 'a3', 'b3'),
+        ('C4', 'C3', 'a12', 'b12'),
+        ('C3', 'C2', 'a1', 'b1'),
+        ('IC1', 'I', 'a10', 'b10'),
+        ('IC2', 'IC1', 'a9', 'b9'),
+        ('IC3', 'IC2', 'a8', 'b8'),
+        ('IC4', 'IC3', 'a11', 'b11'),
+        ('C2', 'C1', 'a2', 'b2'),
+        ('O', 'I', 'a4', 'b4'),
+        ('C2', 'IC2', 'a6', 'b6'),
+        ('C1', 'IC1', 'a5', 'b5'),
+        ('C4', 'IC4', 'a13', 'b13'),
+        ('C3', 'IC3', 'a7', 'b7')
+    ]
+
+    open_state = 'O'
+    shared_variables_dict = {'V': NaN,
+                             'p1': 2.26e-4,
+                             'p2': 0.06990,
+                             'p3': 3.45e-5,
+                             'p4': 0.05462,
+                             'p5': 0.08730,
+                             'p6': 8.91e-3,
+                             'p7': 5.15e-3,
+                             'p8': 0.03158,
+                             'p9': 2.26e-4,
+                             'p10': 0.06990,
+                             'p11': 3.45e-5,
+                             'p12': 0.05462,
+                             'p13': 0.08730,
+                             'p14': 8.91e-3,
+                             'p15': 5.15e-3,
+                             'p16': 0.03158,
+                             'p17': 0.08730,
+                             'p18': 8.91e-3,
+                             'p19': 5.15e-3,
+                             'p20': 0.03158,
+                             'p21': 0.06990,
+                             'p22': 3.45e-5,
+                             'p23': 0.05462,
+                             'p24': 0.08730,
+                             'p25': 8.91e-3,
+                             'p26': 5.15e-3,
+                             'p27': 0.03158,
+                             'p28': 0.08730,
+                             'p29': 8.91e-3,
+                             'p30': 5.15e-3,
+                             'p31': 0.03158,
+                             'p32': 5.15e-3,
+                             'p33': 0.03158,
+                             'p34': 0.03158,
+                             'p35': 8.91e-3,
+                             'p36': 5.15e-3,
+                             'p37': 0.03158,
+                             'p38': 0.08730,
+                             'p39': 8.91e-3,
+                             'p40': 5.15e-3,
+                             'p41': 0.03158,
+                             'p42': 5.15e-3,
+                             'p43': 0.03158,
+                             'p44': 0.03158,
+                             'p45': 0.15240
+                             }
+
+    rate_dictionary = {
+        'a1': ('p1 * exp( p2 * V)',),
+        'b1': ('p3 * exp(-p4 * V)',),
+        'a2': ('p5 * exp( p6 * V)',),
+        'b2': ('p7 * exp(-p8 * V)',),
+        'a3': ('p9 * exp( p10 * V)',),
+        'b3': ('p11 * exp(-p12* V)',),
+        'a4': ('p13 * exp( p14 * V)',),
+        'b4': ('p15 * exp(-p16 * V)',),
+        'a8': ('p17 * exp(p18* V)',),
+        'b8': ('p19 * exp(-p20 * V)',),
+        'a9': ('p21 * exp(p22* V)',),
+        'b9': ('p23 * exp(-p24 * V)',),
+        'a10': ('p25 * exp(p26* V)',),
+        'b10': ('p27 * exp(-p28 * V)',),
+        'a5': ('p29 * exp(p30 * V)',),
+        'b5': ('a10*a5*b4*(b3)/(a3*a4*b10)',),
+        'a6': ('p31 * exp(p32 * V)',),
+        'b6': ('a9*a6*b5*(b2)/(a2*a5*b9)',),
+        'a7': ('p33 * exp(p34 * V)',),
+        'b7': ('a8*a7*b1*(b6)/(a1*a6*b8)',),
+        'a11': ('p35 * exp(p36* V)',),
+        'b11': ('p37 * exp(-p38 * V)',),
+        'a12': ('p39 * exp(p40* V)',),
+        'b12': ('p41 * exp(-p42 * V)',),
+        'a13': ('p43 * exp(p44 * V)',),
+        'b13': ('a13*a11*b7*b12/(a12*a7*b11)',),
+    }
+
+    auxiliary_expression = "p45 * {} * (V - E_Kr)"
+    auxiliary_symbol = 'I_Kr'
+
+    auxiliary_params_dict = {'E_Kr': -85}
+
+    def __init__(self):
+        super().__init__(states=self.states,
+                         open_state=self.open_state,
+                         rates=self.rates,
+                         rate_dictionary=self.rate_dictionary,
+                         auxiliary_expression=self.auxiliary_expression,
+                         auxiliary_symbol=self.auxiliary_symbol,
+                         shared_variables_dict=self.shared_variables_dict,
+                         auxiliary_params_dict=self.auxiliary_params_dict)