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

Updated model

parent a287908d
This diff is collapsed.
......@@ -36,7 +36,22 @@ 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"
......
......@@ -118,20 +118,22 @@ class PhysiBoSSTab(object):
self.svg_plot.children[0].max = self.max_frames.value
def create_dict(self, number_of_files, folder):
"create a dictionary with the states file in the folder 'output', half of the dict is used to calculate the percentage of the node, the other half is for the states"
if number_of_files > 0:
for i in range (0, number_of_files):
if "state_step{0}".format(i) not in self.file_dict.keys():
states_dict = {}
with open(os.path.join(self.output_dir, 'states_%08u.csv' % i), newline='') as csvfile:
states_reader = csv.reader(csvfile, delimiter=',')
for row in states_reader:
if row[0] != 'ID':
states_dict[int(row[0])] = row[1]
self.file_dict["state_step{0}".format(i)] = states_dict
"create a dictionary with the states file in the folder 'output', half of the dict is used to calculate the percentage of the node, the other half is for the states"
if number_of_files > 0:
for i in range (0, number_of_files):
if "state_step{0}".format(i) not in self.file_dict.keys():
states_dict = {}
with open(os.path.join(self.output_dir, 'states_%08u.csv' % i), newline='') as csvfile:
states_reader = csv.reader(csvfile, delimiter=',')
for row in states_reader:
if row[0] != 'ID':
states_dict[int(row[0])] = row[1]
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"
......@@ -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) -->
......@@ -664,7 +667,7 @@
<CD8_Tcell_recruitment_min_signal type="double" units="substrate/micron^3"
description="min concentration to attract CD8 T cells">0.4</CD8_Tcell_recruitment_min_signal> <!-- 0.3 debug -->
<CD8_Tcell_recruitment_saturation_signal type="double" units="substrate/micron^3"
description="saturating concentration to attract CD8 T cells">0.7</CD8_Tcell_recruitment_saturation_signal> <!-- 0.7 debug -->
description="saturating concentration to attract CD8 T cells">0.7</CD8_Tcell_recruitment_saturation_signal> <!-- 0.7 debug -->
<div_initialization type="divider" description="---Initialization Options--"/>
<multiplicity_of_infection type="double" units="none"
......@@ -681,7 +684,13 @@
<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 {