Commit 4a93c8cb authored by Vincent Noël's avatar Vincent Noël
Browse files

Updated model

parent a287908d
This diff is collapsed.
......@@ -36,6 +36,21 @@ if platform.system() != 'Windows':
else:
hublib_flag = False
style = """
<style>
.jupyter-widgets-output-area .output_scroll {
height: unset !important;
border-radius: unset !important;
-webkit-box-shadow: unset !important;
box-shadow: unset !important;
}
.jupyter-widgets-output-area {
height: auto !important;
width: 100%; !important;
}
.container { width:100% !important; }
</style>
"""
# join_our_list = "(Join/ask questions at https://groups.google.com/forum/#!forum/physicell-users)\n"
......
......@@ -133,6 +133,8 @@ class PhysiBoSSTab(object):
self.file_dict["state_step{0}".format(i)] = states_dict
def state_counter(self, number_of_files, percentage, cell_indexes, cell_line):
"create a dict with the states of the network, it can be used to print states pie chart"
self.count_dict = {}
......@@ -188,7 +190,7 @@ class PhysiBoSSTab(object):
all_state = []
a = []
for k in self.count_dict:
state_list.append(list(self.count_dict[k].keys()))
state_list.append([key for key, value in self.count_dict[k].items() if value > 0])
for l in state_list:
for state in l:
all_state.append(state)
......
......@@ -174,52 +174,68 @@ class UserTab(object):
step=0.1,
style=style, layout=widget_layout)
param_name19 = Button(description='m_inhibition_percentage', disabled=True, layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
self.m_inhibition_percentage = FloatText(
value=0.0,
step=0.01,
style=style, layout=widget_layout)
param_name20 = Button(description='fadd_inhibition_percentage', disabled=True, layout=name_button_layout)
param_name20.style.button_color = 'tan'
self.fadd_inhibition_percentage = FloatText(
value=0.0,
step=0.01,
style=style, layout=widget_layout)
div_row3 = Button(description='---Cell Color Options--', disabled=True, layout=divider_button_layout)
param_name19 = Button(description='color_variable', disabled=True, layout=name_button_layout)
param_name19.style.button_color = 'lightgreen'
param_name21 = Button(description='color_variable', disabled=True, layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
self.color_variable = Text(
value='assembled_virion',
style=style, layout=widget_layout)
param_name20 = Button(description='apoptotic_epithelium_color', disabled=True, layout=name_button_layout)
param_name20.style.button_color = 'tan'
param_name22 = Button(description='apoptotic_epithelium_color', disabled=True, layout=name_button_layout)
param_name22.style.button_color = 'tan'
self.apoptotic_epithelium_color = Text(
value='black',
style=style, layout=widget_layout)
param_name21 = Button(description='apoptotic_immune_color', disabled=True, layout=name_button_layout)
param_name21.style.button_color = 'lightgreen'
param_name23 = Button(description='apoptotic_immune_color', disabled=True, layout=name_button_layout)
param_name23.style.button_color = 'lightgreen'
self.apoptotic_immune_color = Text(
value='rosybrown',
style=style, layout=widget_layout)
param_name22 = Button(description='CD8_Tcell_color', disabled=True, layout=name_button_layout)
param_name22.style.button_color = 'tan'
param_name24 = Button(description='CD8_Tcell_color', disabled=True, layout=name_button_layout)
param_name24.style.button_color = 'tan'
self.CD8_Tcell_color = Text(
value='red',
style=style, layout=widget_layout)
param_name23 = Button(description='Macrophage_color', disabled=True, layout=name_button_layout)
param_name23.style.button_color = 'lightgreen'
param_name25 = Button(description='Macrophage_color', disabled=True, layout=name_button_layout)
param_name25.style.button_color = 'lightgreen'
self.Macrophage_color = Text(
value='lime',
style=style, layout=widget_layout)
param_name24 = Button(description='activated_macrophage_color', disabled=True, layout=name_button_layout)
param_name24.style.button_color = 'tan'
param_name26 = Button(description='activated_macrophage_color', disabled=True, layout=name_button_layout)
param_name26.style.button_color = 'tan'
self.activated_macrophage_color = Text(
value='fuchsia',
style=style, layout=widget_layout)
param_name25 = Button(description='Neutrophil_color', disabled=True, layout=name_button_layout)
param_name25.style.button_color = 'lightgreen'
param_name27 = Button(description='Neutrophil_color', disabled=True, layout=name_button_layout)
param_name27.style.button_color = 'lightgreen'
self.Neutrophil_color = Text(
value='cyan',
......@@ -266,9 +282,9 @@ class UserTab(object):
units_button20 = Button(description='percentage', disabled=True, layout=units_button_layout)
units_button20.style.button_color = 'tan'
units_button21 = Button(description='', disabled=True, layout=units_button_layout)
units_button21.style.button_color = 'tan'
units_button21.style.button_color = 'lightgreen'
units_button22 = Button(description='', disabled=True, layout=units_button_layout)
units_button22.style.button_color = 'lightgreen'
units_button22.style.button_color = 'tan'
units_button23 = Button(description='', disabled=True, layout=units_button_layout)
units_button23.style.button_color = 'tan'
units_button24 = Button(description='', disabled=True, layout=units_button_layout)
......@@ -281,6 +297,10 @@ class UserTab(object):
units_button27.style.button_color = 'tan'
units_button28 = Button(description='', disabled=True, layout=units_button_layout)
units_button28.style.button_color = 'lightgreen'
units_button29 = Button(description='', disabled=True, layout=units_button_layout)
units_button29.style.button_color = 'tan'
units_button30 = Button(description='', disabled=True, layout=units_button_layout)
units_button30.style.button_color = 'lightgreen'
desc_button1 = Button(description='' , tooltip='', disabled=True, layout=desc_button_layout)
desc_button1.style.button_color = 'lightgreen'
......@@ -318,20 +338,24 @@ class UserTab(object):
desc_button17.style.button_color = 'lightgreen'
desc_button18 = Button(description='percentage of tissue sitting above blood vessels' , tooltip='percentage of tissue sitting above blood vessels', disabled=True, layout=desc_button_layout)
desc_button18.style.button_color = 'tan'
desc_button19 = Button(description='color cells based on this variable' , tooltip='color cells based on this variable', disabled=True, layout=desc_button_layout)
desc_button19 = Button(description='ratio of the population capable of inhibiting M protein' , tooltip='ratio of the population capable of inhibiting M protein', disabled=True, layout=desc_button_layout)
desc_button19.style.button_color = 'lightgreen'
desc_button20 = Button(description='apoptotic epithelial cell color' , tooltip='apoptotic epithelial cell color', disabled=True, layout=desc_button_layout)
desc_button20 = Button(description='ratio of the population capable of inhibiting FADD protein' , tooltip='ratio of the population capable of inhibiting FADD protein', disabled=True, layout=desc_button_layout)
desc_button20.style.button_color = 'tan'
desc_button21 = Button(description='apoptotic immune cell color' , tooltip='apoptotic immune cell color', disabled=True, layout=desc_button_layout)
desc_button21 = Button(description='color cells based on this variable' , tooltip='color cells based on this variable', disabled=True, layout=desc_button_layout)
desc_button21.style.button_color = 'lightgreen'
desc_button22 = Button(description='CD8 T cell color' , tooltip='CD8 T cell color', disabled=True, layout=desc_button_layout)
desc_button22 = Button(description='apoptotic epithelial cell color' , tooltip='apoptotic epithelial cell color', disabled=True, layout=desc_button_layout)
desc_button22.style.button_color = 'tan'
desc_button23 = Button(description='macrophage color' , tooltip='macrophage color', disabled=True, layout=desc_button_layout)
desc_button23 = Button(description='apoptotic immune cell color' , tooltip='apoptotic immune cell color', disabled=True, layout=desc_button_layout)
desc_button23.style.button_color = 'lightgreen'
desc_button24 = Button(description='color of activated macrophage' , tooltip='color of activated macrophage', disabled=True, layout=desc_button_layout)
desc_button24 = Button(description='CD8 T cell color' , tooltip='CD8 T cell color', disabled=True, layout=desc_button_layout)
desc_button24.style.button_color = 'tan'
desc_button25 = Button(description='neutrophil color' , tooltip='neutrophil color', disabled=True, layout=desc_button_layout)
desc_button25 = Button(description='macrophage color' , tooltip='macrophage color', disabled=True, layout=desc_button_layout)
desc_button25.style.button_color = 'lightgreen'
desc_button26 = Button(description='color of activated macrophage' , tooltip='color of activated macrophage', disabled=True, layout=desc_button_layout)
desc_button26.style.button_color = 'tan'
desc_button27 = Button(description='neutrophil color' , tooltip='neutrophil color', disabled=True, layout=desc_button_layout)
desc_button27.style.button_color = 'lightgreen'
row1 = [param_name1, self.random_seed, units_button1, desc_button1]
row2 = [param_name2, self.immune_dt, units_button3, desc_button2]
......@@ -351,13 +375,15 @@ class UserTab(object):
row16 = [param_name16, self.number_of_macrophages, units_button18, desc_button16]
row17 = [param_name17, self.number_of_neutrophils, units_button19, desc_button17]
row18 = [param_name18, self.perecentage_tissue_vascularized, units_button20, desc_button18]
row19 = [param_name19, self.color_variable, units_button22, desc_button19]
row20 = [param_name20, self.apoptotic_epithelium_color, units_button23, desc_button20]
row21 = [param_name21, self.apoptotic_immune_color, units_button24, desc_button21]
row22 = [param_name22, self.CD8_Tcell_color, units_button25, desc_button22]
row23 = [param_name23, self.Macrophage_color, units_button26, desc_button23]
row24 = [param_name24, self.activated_macrophage_color, units_button27, desc_button24]
row25 = [param_name25, self.Neutrophil_color, units_button28, desc_button25]
row19 = [param_name19, self.m_inhibition_percentage, units_button21, desc_button19]
row20 = [param_name20, self.fadd_inhibition_percentage, units_button22, desc_button20]
row21 = [param_name21, self.color_variable, units_button24, desc_button21]
row22 = [param_name22, self.apoptotic_epithelium_color, units_button25, desc_button22]
row23 = [param_name23, self.apoptotic_immune_color, units_button26, desc_button23]
row24 = [param_name24, self.CD8_Tcell_color, units_button27, desc_button24]
row25 = [param_name25, self.Macrophage_color, units_button28, desc_button25]
row26 = [param_name26, self.activated_macrophage_color, units_button29, desc_button26]
row27 = [param_name27, self.Neutrophil_color, units_button30, desc_button27]
box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%')
box1 = Box(children=row1, layout=box_layout)
......@@ -385,6 +411,8 @@ class UserTab(object):
box23 = Box(children=row23, layout=box_layout)
box24 = Box(children=row24, layout=box_layout)
box25 = Box(children=row25, layout=box_layout)
box26 = Box(children=row26, layout=box_layout)
box27 = Box(children=row27, layout=box_layout)
self.tab = VBox([
box1,
......@@ -407,14 +435,16 @@ class UserTab(object):
box16,
box17,
box18,
div_row3,
box19,
box20,
div_row3,
box21,
box22,
box23,
box24,
box25,
box26,
box27,
])
# Populate the GUI widgets with values from the XML
......@@ -444,6 +474,8 @@ class UserTab(object):
self.number_of_macrophages.value = int(uep.find('.//number_of_macrophages').text)
self.number_of_neutrophils.value = int(uep.find('.//number_of_neutrophils').text)
self.perecentage_tissue_vascularized.value = float(uep.find('.//perecentage_tissue_vascularized').text)
self.m_inhibition_percentage.value = float(uep.find('.//m_inhibition_percentage').text)
self.fadd_inhibition_percentage.value = float(uep.find('.//fadd_inhibition_percentage').text)
self.color_variable.value = (uep.find('.//color_variable').text)
self.apoptotic_epithelium_color.value = (uep.find('.//apoptotic_epithelium_color').text)
self.apoptotic_immune_color.value = (uep.find('.//apoptotic_immune_color').text)
......@@ -480,6 +512,8 @@ class UserTab(object):
uep.find('.//number_of_macrophages').text = str(self.number_of_macrophages.value)
uep.find('.//number_of_neutrophils').text = str(self.number_of_neutrophils.value)
uep.find('.//perecentage_tissue_vascularized').text = str(self.perecentage_tissue_vascularized.value)
uep.find('.//m_inhibition_percentage').text = str(self.m_inhibition_percentage.value)
uep.find('.//fadd_inhibition_percentage').text = str(self.fadd_inhibition_percentage.value)
uep.find('.//color_variable').text = str(self.color_variable.value)
uep.find('.//apoptotic_epithelium_color').text = str(self.apoptotic_epithelium_color.value)
uep.find('.//apoptotic_immune_color').text = str(self.apoptotic_immune_color.value)
......
......@@ -405,6 +405,9 @@
<activated_immune_cell units="dimensionless" type="double"
description="used internally to track activation state">0.0</activated_immune_cell>
<virus_expression_threshold units="dimensionless" type="double"
description="minimal quantity of virus to activate virus_expression node">10.0</virus_expression_threshold>
<!-- your custom data and parameters go here (for new submodels) -->
......@@ -682,6 +685,12 @@
<perecentage_tissue_vascularized units="percentage" type="double"
description="percentage of tissue sitting above blood vessels">8.8</perecentage_tissue_vascularized>
<m_inhibition_percentage units="dimensionless" type="double"
description="ratio of the population capable of inhibiting M protein">0.0</m_inhibition_percentage>
<fadd_inhibition_percentage units="dimensionless" type="double"
description="ratio of the population capable of inhibiting FADD protein">0.0</fadd_inhibition_percentage>
<div_colors type="divider" description="---Cell Color Options--"/>
<color_variable type="string" description="color cells based on this variable">assembled_virion</color_variable>
......
......@@ -10,8 +10,8 @@ Node Chemokin_secretion {
logic = Virus_inside;
}
Node Virus_damage {
logic = Virus_damage;
Node Virus_expression {
logic = Virus_expression;
}
Node TCell_attached {
......@@ -21,215 +21,266 @@ Node TCell_attached {
Node FAS_FASL_complex {
logic = (TCell_attached);
rate_up = @logic ? $u_FAS_FASL_complex : 0;
rate_down = @logic ? 0 : $d_FAS_FASL_complex;
rate_up = ( $FAS_FASL_complex_ko ? 0.0 : ( $FAS_FASL_complex_up ? @max_rate : ( @logic ? $u_FAS_FASL_complex : 0)));
rate_down = ( $FAS_FASL_complex_ko ? @max_rate : ( $FAS_FASL_complex_up ? 0.0 : ( @logic ? 0 : $d_FAS_FASL_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node BAD_BBC3_BCL2L11_complex {
logic = (BCL2_MCL1_BCL2L1_complex);
rate_up = @logic ? $u_BAD_BBC3_BCL2L11_complex : 0;
rate_down = @logic ? 0 : $d_BAD_BBC3_BCL2L11_complex;
rate_up = ( $BAD_BBC3_BCL2L11_complex_ko ? 0.0 : ( $BAD_BBC3_BCL2L11_complex_up ? @max_rate : ( @logic ? $u_BAD_BBC3_BCL2L11_complex : 0)));
rate_down = ( $BAD_BBC3_BCL2L11_complex_ko ? @max_rate : ( $BAD_BBC3_BCL2L11_complex_up ? 0.0 : ( @logic ? 0 : $d_BAD_BBC3_BCL2L11_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node Apoptosome_complex {
logic = (CYCS & APAF1 & !AKT1 & CASP9_Cytoplasm_input);
rate_up = @logic ? $u_Apoptosome_complex : 0;
rate_down = @logic ? 0 : $d_Apoptosome_complex;
logic = ((( CYCS & APAF1 & CASP9_Cytoplasm_input ) | Unknown_mechanism ) & !AKT1 );
rate_up = ( $Apoptosome_complex_ko ? 0.0 : ( $Apoptosome_complex_up ? @max_rate : ( @logic ? $u_Apoptosome_complex : 0)));
rate_down = ( $Apoptosome_complex_ko ? @max_rate : ( $Apoptosome_complex_up ? 0.0 : ( @logic ? 0 : $d_Apoptosome_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node TNF_TNFRSF1A_complex {
logic = (TNF_TNFRSF1A_complex);
rate_up = @logic ? $u_TNF_TNFRSF1A_complex : 0;
rate_down = @logic ? 0 : $d_TNF_TNFRSF1A_complex;
rate_up = ( $TNF_TNFRSF1A_complex_ko ? 0.0 : ( $TNF_TNFRSF1A_complex_up ? @max_rate : ( @logic ? $u_TNF_TNFRSF1A_complex : 0)));
rate_down = ( $TNF_TNFRSF1A_complex_ko ? @max_rate : ( $TNF_TNFRSF1A_complex_up ? 0.0 : ( @logic ? 0 : $d_TNF_TNFRSF1A_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node TRADD_FADD_complex {
logic = (TNF_TNFRSF1A_complex & FADD & TRADD);
rate_up = @logic ? $u_TRADD_FADD_complex : 0;
rate_down = @logic ? 0 : $d_TRADD_FADD_complex;
rate_up = ( $TRADD_FADD_complex_ko ? 0.0 : ( $TRADD_FADD_complex_up ? @max_rate : ( @logic ? $u_TRADD_FADD_complex : 0)));
rate_down = ( $TRADD_FADD_complex_ko ? @max_rate : ( $TRADD_FADD_complex_up ? 0.0 : ( @logic ? 0 : $d_TRADD_FADD_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node BCL2_MCL1_BCL2L1_complex {
logic = (!Orf7a & E & !BAD) | (Orf7a & !BAD);
rate_up = @logic ? $u_BCL2_MCL1_BCL2L1_complex : 0;
rate_down = @logic ? 0 : $d_BCL2_MCL1_BCL2L1_complex;
rate_up = ( $BCL2_MCL1_BCL2L1_complex_ko ? 0.0 : ( $BCL2_MCL1_BCL2L1_complex_up ? @max_rate : ( @logic ? $u_BCL2_MCL1_BCL2L1_complex : 0)));
rate_down = ( $BCL2_MCL1_BCL2L1_complex_ko ? @max_rate : ( $BCL2_MCL1_BCL2L1_complex_up ? 0.0 : ( @logic ? 0 : $d_BCL2_MCL1_BCL2L1_complex)));
max_rate = 1.7976931348623157E+308/1;
}
Node FADD {
logic = (FAS_FASL_complex);
rate_up = @logic ? $u_FADD : 0;
rate_down = @logic ? 0 : $d_FADD;
rate_up = ( $FADD_ko ? 0.0 : ( $FADD_up ? @max_rate : ( @logic ? $u_FADD : 0)));
rate_down = ( $FADD_ko ? @max_rate : ( $FADD_up ? 0.0 : ( @logic ? 0 : $d_FADD)));
max_rate = 1.7976931348623157E+308/1;
}
Node CASP8 {
logic = (!TRADD_FADD_complex & FADD) | (TRADD_FADD_complex);
rate_up = @logic ? $u_CASP8 : 0;
rate_down = @logic ? 0 : $d_CASP8;
rate_up = ( $CASP8_ko ? 0.0 : ( $CASP8_up ? @max_rate : ( @logic ? $u_CASP8 : 0)));
rate_down = ( $CASP8_ko ? @max_rate : ( $CASP8_up ? 0.0 : ( @logic ? 0 : $d_CASP8)));
max_rate = 1.7976931348623157E+308/1;
}
Node CASP3 {
logic = ( CASP9_Cytoplasm | CASP8);
rate_up = @logic ? $u_CASP3 : 0;
rate_down = @logic ? 0 : $d_CASP3;
logic = ( CASP9_Cytoplasm | CASP8 );
rate_up = ( $CASP3_ko ? 0.0 : ( $CASP3_up ? @max_rate : ( @logic ? $u_CASP3 : 0)));
rate_down = ( $CASP3_ko ? @max_rate : ( $CASP3_up ? 0.0 : ( @logic ? 0 : $d_CASP3)));
max_rate = 1.7976931348623157E+308/1;
}
Node CASP9_Cytoplasm_input {
logic = (CASP9_Cytoplasm_input);
rate_up = @logic ? $u_CASP9_Cytoplasm_input : 0;
rate_down = @logic ? 0 : $d_CASP9_Cytoplasm_input;
rate_up = ( $CASP9_Cytoplasm_input_ko ? 0.0 : ( $CASP9_Cytoplasm_input_up ? @max_rate : ( @logic ? $u_CASP9_Cytoplasm_input : 0)));
rate_down = ( $CASP9_Cytoplasm_input_ko ? @max_rate : ( $CASP9_Cytoplasm_input_up ? 0.0 : ( @logic ? 0 : $d_CASP9_Cytoplasm_input)));
max_rate = 1.7976931348623157E+308/1;
}
Node CASP9_Cytoplasm {
logic = (Apoptosome_complex & !AKT1);
rate_up = @logic ? $u_CASP9_Cytoplasm : 0;
rate_down = @logic ? 0 : $d_CASP9_Cytoplasm;
rate_up = ( $CASP9_Cytoplasm_ko ? 0.0 : ( $CASP9_Cytoplasm_up ? @max_rate : ( @logic ? $u_CASP9_Cytoplasm : 0)));
rate_down = ( $CASP9_Cytoplasm_ko ? @max_rate : ( $CASP9_Cytoplasm_up ? 0.0 : ( @logic ? 0 : $d_CASP9_Cytoplasm)));
max_rate = 1.7976931348623157E+308/1;
}
Node BID {
logic = (CASP8);
rate_up = @logic ? $u_BID : 0;
rate_down = @logic ? 0 : $d_BID;
rate_up = ( $BID_ko ? 0.0 : ( $BID_up ? @max_rate : ( @logic ? $u_BID : 0)));
rate_down = ( $BID_ko ? @max_rate : ( $BID_up ? 0.0 : ( @logic ? 0 : $d_BID)));
max_rate = 1.7976931348623157E+308/1;
}
Node CYCS {
logic = (MAPK14);
rate_up = @logic ? $u_CYCS : 0;
rate_down = @logic ? 0 : $d_CYCS;
logic = (MAPK14 | MOMP);
rate_up = ( $CYCS_ko ? 0.0 : ( $CYCS_up ? @max_rate : ( @logic ? $u_CYCS : 0)));
rate_down = ( $CYCS_ko ? @max_rate : ( $CYCS_up ? 0.0 : ( @logic ? 0 : $d_CYCS)));
max_rate = 1.7976931348623157E+308/1;
}
Node APAF1 {
logic = (BAX);
rate_up = @logic ? $u_APAF1 : 0;
rate_down = @logic ? 0 : $d_APAF1;
rate_up = ( $APAF1_ko ? 0.0 : ( $APAF1_up ? @max_rate : ( @logic ? $u_APAF1 : 0)));
rate_down = ( $APAF1_ko ? @max_rate : ( $APAF1_up ? 0.0 : ( @logic ? 0 : $d_APAF1)));
max_rate = 1.7976931348623157E+308/1;
}
Node AKT1 {
logic = (!M);
rate_up = @logic ? $u_AKT1 : 0;
rate_down = @logic ? 0 : $d_AKT1;
rate_up = ( $AKT1_ko ? 0.0 : ( $AKT1_up ? @max_rate : ( @logic ? $u_AKT1 : 0)));
rate_down = ( $AKT1_ko ? @max_rate : ( $AKT1_up ? 0.0 : ( @logic ? 0 : $d_AKT1)));
max_rate = 1.7976931348623157E+308/1;
}
Node BAX {
logic = (!BAD_BBC3_BCL2L11_complex & !BCL2_MCL1_BCL2L1_complex & BID) | (BAD_BBC3_BCL2L11_complex & !BCL2_MCL1_BCL2L1_complex);
rate_up = @logic ? $u_BAX : 0;
rate_down = @logic ? 0 : $d_BAX;
}
Node CASP7 {
logic = (!CASP8 & CASP9_Cytoplasm) | (CASP8);
rate_up = @logic ? $u_CASP7 : 0;
rate_down = @logic ? 0 : $d_CASP7;
rate_up = ( $BAX_ko ? 0.0 : ( $BAX_up ? @max_rate : ( @logic ? $u_BAX : 0)));
rate_down = ( $BAX_ko ? @max_rate : ( $BAX_up ? 0.0 : ( @logic ? 0 : $d_BAX)));
max_rate = 1.7976931348623157E+308/1;
}
Node Apoptosis_phenotype {
logic = (!CASP3 & !CASP7 & !Orf3b & !Orf8a & !N & !Orf6 & !S & Orf9b) | (!CASP3 & !CASP7 & !Orf3b & !Orf8a & !N & !Orf6 & S) | (!CASP3 & !CASP7 & !Orf3b & !Orf8a & !N & Orf6) | (!CASP3 & !CASP7 & !Orf3b & !Orf8a & N) | (!CASP3 & !CASP7 & !Orf3b & Orf8a) | (!CASP3 & !CASP7 & Orf3b) | (!CASP3 & CASP7) | (CASP3);
logic = (CASP3);
rate_up = @logic ? $u_Apoptosis_phenotype : 0;
rate_down = @logic ? 0 : $d_Apoptosis_phenotype;
}
Node M {
logic = (Virus_damage);
rate_up = @logic ? $u_M : 0;
rate_down = @logic ? 0 : $d_M;
logic = (Virus_expression);
rate_up = ( $M_ko ? 0.0 : ( $M_up ? @max_rate : ( @logic ? $u_M : 0)));
rate_down = ( $M_ko ? @max_rate : ( $M_up ? 0.0 : ( @logic ? 0 : $d_M)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf7a {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf7a : 0;
rate_down = @logic ? 0 : $d_Orf7a;
logic = (Virus_expression);
rate_up = ( $Orf7a_ko ? 0.0 : ( $Orf7a_up ? @max_rate : ( @logic ? $u_Orf7a : 0)));
rate_down = ( $Orf7a_ko ? @max_rate : ( $Orf7a_up ? 0.0 : ( @logic ? 0 : $d_Orf7a)));
max_rate = 1.7976931348623157E+308/1;
}
Node TRADD {
logic = (TRADD);
rate_up = @logic ? $u_TRADD : 0;
rate_down = @logic ? 0 : $d_TRADD;
rate_up = ( $TRADD_ko ? 0.0 : ( $TRADD_up ? @max_rate : ( @logic ? $u_TRADD : 0)));
rate_down = ( $TRADD_ko ? @max_rate : ( $TRADD_up ? 0.0 : ( @logic ? 0 : $d_TRADD)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf3a {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf3a : 0;
rate_down = @logic ? 0 : $d_Orf3a;
logic = (Virus_expression);
rate_up = ( $Orf3a_ko ? 0.0 : ( $Orf3a_up ? @max_rate : ( @logic ? $u_Orf3a : 0)));
rate_down = ( $Orf3a_ko ? @max_rate : ( $Orf3a_up ? 0.0 : ( @logic ? 0 : $d_Orf3a)));
max_rate = 1.7976931348623157E+308/1;
}
Node MAPK14 {
logic = (Orf3a);
rate_up = @logic ? $u_MAPK14 : 0;
rate_down = @logic ? 0 : $d_MAPK14;
rate_up = ( $MAPK14_ko ? 0.0 : ( $MAPK14_up ? @max_rate : ( @logic ? $u_MAPK14 : 0)));
rate_down = ( $MAPK14_ko ? @max_rate : ( $MAPK14_up ? 0.0 : ( @logic ? 0 : $d_MAPK14)));
max_rate = 1.7976931348623157E+308/1;
}
Node E {
logic = (Virus_damage);
rate_up = @logic ? $u_E : 0;
rate_down = @logic ? 0 : $d_E;
logic = (Virus_expression);
rate_up = ( $E_ko ? 0.0 : ( $E_up ? @max_rate : ( @logic ? $u_E : 0)));
rate_down = ( $E_ko ? @max_rate : ( $E_up ? 0.0 : ( @logic ? 0 : $d_E)));
max_rate = 1.7976931348623157E+308/1;
}
Node BAD {
logic = (!AKT1);
rate_up = ( $BAD_ko ? 0.0 : ( $BAD_up ? @max_rate : ( @logic ? $u_BAD : 0)));
rate_down = ( $BAD_ko ? @max_rate : ( $BAD_up ? 0.0 : ( @logic ? 0 : $d_BAD)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf3b {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf3b : 0;
rate_down = @logic ? 0 : $d_Orf3b;
logic = (Virus_expression);
rate_up = ( $Orf3b_ko ? 0.0 : ( $Orf3b_up ? @max_rate : ( @logic ? $u_Orf3b : 0)));
rate_down = ( $Orf3b_ko ? @max_rate : ( $Orf3b_up ? 0.0 : ( @logic ? 0 : $d_Orf3b)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf8a {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf8a : 0;
rate_down = @logic ? 0 : $d_Orf8a;
logic = (Virus_expression);
rate_up = ( $Orf8a_ko ? 0.0 : ( $Orf8a_up ? @max_rate : ( @logic ? $u_Orf8a : 0)));
rate_down = ( $Orf8a_ko ? @max_rate : ( $Orf8a_up ? 0.0 : ( @logic ? 0 : $d_Orf8a)));
max_rate = 1.7976931348623157E+308/1;
}
Node N {
logic = (Virus_damage);
rate_up = @logic ? $u_N : 0;
rate_down = @logic ? 0 : $d_N;
logic = (Virus_expression);
rate_up = ( $N_ko ? 0.0 : ( $N_up ? @max_rate : ( @logic ? $u_N : 0)));
rate_down = ( $N_ko ? @max_rate : ( $N_up ? 0.0 : ( @logic ? 0 : $d_N)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf6 {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf6 : 0;
rate_down = @logic ? 0 : $d_Orf6;
logic = (Virus_expression);
rate_up = ( $Orf6_ko ? 0.0 : ( $Orf6_up ? @max_rate : ( @logic ? $u_Orf6 : 0)));
rate_down = ( $Orf6_ko ? @max_rate : ( $Orf6_up ? 0.0 : ( @logic ? 0 : $d_Orf6)));
max_rate = 1.7976931348623157E+308/1;
}
Node S {
logic = (Virus_damage);
rate_up = @logic ? $u_S : 0;
rate_down = @logic ? 0 : $d_S;
logic = (Virus_expression);
rate_up = ( $S_ko ? 0.0 : ( $S_up ? @max_rate : ( @logic ? $u_S : 0)));
rate_down = ( $S_ko ? @max_rate : ( $S_up ? 0.0 : ( @logic ? 0 : $d_S)));
max_rate = 1.7976931348623157E+308/1;
}
Node Orf9b {
logic = (Virus_damage);
rate_up = @logic ? $u_Orf9b : 0;
rate_down = @logic ? 0 : $d_Orf9b;
logic = (Virus_expression);
rate_up = ( $Orf9b_ko ? 0.0 : ( $Orf9b_up ? @max_rate : ( @logic ? $u_Orf9b : 0)));
rate_down = ( $Orf9b_ko ? @max_rate : ( $Orf9b_up ? 0.0 : ( @logic ? 0 : $d_Orf9b)));
max_rate = 1.7976931348623157E+308/1;
}
Node Unknown_mechanism {
Node BAD {
logic = ( Orf3b | Orf8a | N | Orf6 | S | Orf9b );
rate_up = ( $Unknown_mechanism_ko ? 0.0 : ( $Unknown_mechanism_up ? @max_rate : ( @logic ? $u_Unknown_mechanism : 0)));
rate_down = ( $Unknown_mechanism_ko ? @max_rate : ( $Unknown_mechanism_up ? 0.0 : ( @logic ? 0 : $d_Unknown_mechanism)));
max_rate = 1.7976931348623157E+308/1;
}
logic = (!AKT1);
rate_up = @logic ? $u_BAD : 0;
rate_down = @logic ? 0 : $d_BAD;
Node Apoptosis_type_I {
logic = ( Apoptosis_phenotype & CASP8 & !Apoptosis_type_II);