# This file is auto-generated from a Python script that parses a PhysiCell configuration (.xml) file. # # Edit at your own risk. # import os from ipywidgets import Label,Text,Checkbox,Button,HBox,VBox,FloatText,IntText,BoundedIntText,BoundedFloatText,Layout,Box,Dropdown class CellTypesTab(object): def __init__(self): micron_units = Label('micron') # use "option m" (Mac, for micro symbol) constWidth = '180px' tab_height = '500px' stepsize = 10 #style = {'description_width': '250px'} style = {'description_width': '25%'} layout = {'width': '400px'} name_button_layout={'width':'25%'} widget_layout = {'width': '15%'} widget_layout_long = {'width': '20%'} units_button_layout ={'width':'15%'} desc_button_layout={'width':'45%'} divider_button_layout={'width':'40%'} divider_button_layout={'width':'60%'} box_layout = Layout(display='flex', flex_flow='row', align_items='stretch', width='100%') self.cell_type_dropdown = Dropdown(description='Cell type:',) self.cell_type_dropdown.style = {'description_width': '%sch' % str(len(self.cell_type_dropdown.description) + 1)} cell_type_names_layout={'width':'30%'} cell_type_names_style={'description_width':'initial'} self.parent_name = Text(value='None',description='inherits properties from parent type:',disabled=True, style=cell_type_names_style, layout=cell_type_names_layout) explain_inheritance = Label(value=' This cell line inherits its properties from its parent type. Any settings below override those inherited properties.') # , style=cell_type_names_style, layout=cell_type_names_layout) self.cell_type_parent_row = HBox([self.cell_type_dropdown, self.parent_name]) self.cell_type_parent_dict = {} self.cell_type_dict = {} self.cell_type_dict['default'] = 'default' self.cell_type_dict['lung epithelium'] = 'lung epithelium' self.cell_type_dict['immune'] = 'immune' self.cell_type_dict['CD8 Tcell'] = 'CD8 Tcell' self.cell_type_dict['macrophage'] = 'macrophage' self.cell_type_dict['neutrophil'] = 'neutrophil' self.cell_type_dropdown.options = self.cell_type_dict self.cell_type_dropdown.observe(self.cell_type_cb) self.cell_type_parent_dict['default'] = 'None' self.cell_type_parent_dict['lung epithelium'] = 'default' self.cell_type_parent_dict['immune'] = 'default' self.cell_type_parent_dict['CD8 Tcell'] = 'immune' self.cell_type_parent_dict['macrophage'] = 'immune' self.cell_type_parent_dict['neutrophil'] = 'immune' self.cell_def_vboxes = [] self.bnd_filenames = [None]*6 self.cfg_filenames = [None]*6 # >>>>>>>>>>>>>>>>> = default # ------------------------- div_row1 = Button(description='phenotype:cycle (model: flow_cytometry_separated_cycle_model; code=6)', disabled=True, layout=divider_button_layout) div_row1.style.button_color = 'orange' name_btn = Button(description='Phase 0 -> Phase 1 transition rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float0 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float0, units_btn, ] box0 = Box(children=row, layout=box_layout) name_btn = Button(description='Phase 1 -> Phase 2 transition rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float1 = FloatText(value='0.00208333', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float1, units_btn, ] box1 = Box(children=row, layout=box_layout) name_btn = Button(description='Phase 2 -> Phase 3 transition rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float2 = FloatText(value='0.00416667', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float2, units_btn, ] box2 = Box(children=row, layout=box_layout) name_btn = Button(description='Phase 3 -> Phase 0 transition rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float3 = FloatText(value='0.0166667', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float3, units_btn, ] box3 = Box(children=row, layout=box_layout) # ------------------------- div_row2 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row2.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float4 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float4, units_btn, ] box4 = Box(children=row, layout=box_layout) name_btn = Button(description='unlysed_fluid_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float5 = FloatText(value='0.05', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float5, units_btn, ] box5 = Box(children=row, layout=box_layout) name_btn = Button(description='lysed_fluid_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float6 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float6, units_btn, ] box6 = Box(children=row, layout=box_layout) name_btn = Button(description='cytoplasmic_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float7 = FloatText(value='1.66667e-02', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float7, units_btn, ] box7 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float8 = FloatText(value='5.83333e-03', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float8, units_btn, ] box8 = Box(children=row, layout=box_layout) name_btn = Button(description='calcification_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float9 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float9, units_btn, ] box9 = Box(children=row, layout=box_layout) name_btn = Button(description='relative_rupture_volume', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float10 = FloatText(value='2.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float10, units_btn, ] box10 = Box(children=row, layout=box_layout) death_model2 = Button(description='model: necrosis', disabled=True, layout={'width':'30%'}) death_model2.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float11 = FloatText(value='0.0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float11, units_btn, ] box11 = Box(children=row, layout=box_layout) name_btn = Button(description='unlysed_fluid_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float12 = FloatText(value='0.05', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float12, units_btn, ] box12 = Box(children=row, layout=box_layout) name_btn = Button(description='lysed_fluid_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float13 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float13, units_btn, ] box13 = Box(children=row, layout=box_layout) name_btn = Button(description='cytoplasmic_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float14 = FloatText(value='1.66667e-02', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float14, units_btn, ] box14 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float15 = FloatText(value='5.83333e-03', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float15, units_btn, ] box15 = Box(children=row, layout=box_layout) name_btn = Button(description='calcification_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float16 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float16, units_btn, ] box16 = Box(children=row, layout=box_layout) name_btn = Button(description='relative_rupture_volume', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float17 = FloatText(value='2.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float17, units_btn, ] box17 = Box(children=row, layout=box_layout) # ------------------------- div_row3 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout) div_row3.style.button_color = 'orange' name_btn = Button(description='total', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float18 = FloatText(value='2494', step='100', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float18, units_btn, ] box18 = Box(children=row, layout=box_layout) name_btn = Button(description='fluid_fraction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float19 = FloatText(value='0.75', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float19, units_btn, ] box19 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float20 = FloatText(value='540', step='10', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float20, units_btn, ] box20 = Box(children=row, layout=box_layout) name_btn = Button(description='fluid_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float21 = FloatText(value='0.05', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float21, units_btn, ] box21 = Box(children=row, layout=box_layout) name_btn = Button(description='cytoplasmic_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float22 = FloatText(value='0.0045', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float22, units_btn, ] box22 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float23 = FloatText(value='0.0055', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float23, units_btn, ] box23 = Box(children=row, layout=box_layout) name_btn = Button(description='calcified_fraction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float24 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float24, units_btn, ] box24 = Box(children=row, layout=box_layout) name_btn = Button(description='calcification_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float25 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float25, units_btn, ] box25 = Box(children=row, layout=box_layout) name_btn = Button(description='relative_rupture_volume', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float26 = FloatText(value='2.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float26, units_btn, ] box26 = Box(children=row, layout=box_layout) # ------------------------- div_row4 = Button(description='phenotype:mechanics', disabled=True, layout=divider_button_layout) div_row4.style.button_color = 'orange' name_btn = Button(description='cell_cell_adhesion_strength', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float27 = FloatText(value='0.4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float27, units_btn, ] box27 = Box(children=row, layout=box_layout) name_btn = Button(description='cell_cell_repulsion_strength', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float28 = FloatText(value='10.0', step='1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float28, units_btn, ] box28 = Box(children=row, layout=box_layout) name_btn = Button(description='relative_maximum_adhesion_distance', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float29 = FloatText(value='1.25', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float29, units_btn, ] box29 = Box(children=row, layout=box_layout) self.bool0 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='set_relative_equilibrium_distance', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float30 = FloatText(value='1.8', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [self.bool0, name_btn, self.float30, units_btn, ] box30 = Box(children=row, layout=box_layout) self.bool1 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='set_absolute_equilibrium_distance', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float31 = FloatText(value='15.12', step='1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [self.bool1, name_btn, self.float31, units_btn, ] box31 = Box(children=row, layout=box_layout) # ------------------------- div_row5 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row5.style.button_color = 'orange' name_btn = Button(description='speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float32 = FloatText(value='4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float32, units_btn] box32 = Box(children=row, layout=box_layout) name_btn = Button(description='persistence_time', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float33 = FloatText(value='5', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float33, units_btn] box33 = Box(children=row, layout=box_layout) name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float34 = FloatText(value='0.7', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float34, units_btn] box34 = Box(children=row, layout=box_layout) self.bool2 = Checkbox(description='enabled', value=False,layout=name_button_layout) self.bool3 = Checkbox(description='use_2D', value=True,layout=name_button_layout) chemotaxis_btn = Button(description='chemotaxis', disabled=True, layout={'width':'30%'}) chemotaxis_btn.style.button_color = '#ffde6b' self.bool4 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.chemotaxis_substrate1 = Text(value='chemokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_substrate1] box35 = Box(children=row, layout=box_layout) name_btn = Button(description='direction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.chemotaxis_direction1 = Text(value='1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_direction1] box36 = Box(children=row, layout=box_layout) # ------------------------- div_row6 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout) div_row6.style.button_color = 'orange' name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text0 = Text(value='interferon 1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text0] box37 = Box(children=row, layout=box_layout) name_btn = Button(description='secretion_target', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float35 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless substrate concentration', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float35, units_btn] box38 = Box(children=row, layout=box_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text1 = Text(value='pro-inflammatory cytokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text1] box39 = Box(children=row, layout=box_layout) name_btn = Button(description='secretion_target', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float36 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless substrate concentration', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float36, units_btn] box40 = Box(children=row, layout=box_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text2 = Text(value='chemokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text2] box41 = Box(children=row, layout=box_layout) name_btn = Button(description='secretion_target', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float37 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless substrate concentration', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float37, units_btn] box42 = Box(children=row, layout=box_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text3 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text3] box43 = Box(children=row, layout=box_layout) name_btn = Button(description='secretion_target', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float38 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless substrate concentration', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float38, units_btn] box44 = Box(children=row, layout=box_layout) # ------------------------- div_row7 = Button(description='phenotype:molecular', disabled=True, layout=divider_button_layout) div_row7.style.button_color = 'orange' # ================== , if present ================== div_row8 = Button(description='Custom Data',disabled=True, layout=divider_button_layout) div_row8.style.button_color = 'cyan' name_btn = Button(description='virion', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float39 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='virions', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='endocytosed virions', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float39, units_btn, description_btn] box45 = Box(children=row, layout=box_layout) name_btn = Button(description='uncoated_virion', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float40 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='virions', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='uncoated endocytosed virions', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float40, units_btn, description_btn] box46 = Box(children=row, layout=box_layout) name_btn = Button(description='viral_RNA', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float41 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='RNA', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='total (functional) viral RNA copies', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float41, units_btn, description_btn] box47 = Box(children=row, layout=box_layout) name_btn = Button(description='viral_protein', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float42 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='protein', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='total assembled sets of viral protein', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float42, units_btn, description_btn] box48 = Box(children=row, layout=box_layout) name_btn = Button(description='assembled_virion', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float43 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='total assembled virions', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float43, units_btn, description_btn] box49 = Box(children=row, layout=box_layout) name_btn = Button(description='virion_uncoating_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float44 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate at which an internalized virion is uncoated', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float44, units_btn, description_btn] box50 = Box(children=row, layout=box_layout) name_btn = Button(description='uncoated_to_RNA_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float45 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='rate at which uncoated virion makes its mRNA available', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float45, units_btn, description_btn] box51 = Box(children=row, layout=box_layout) name_btn = Button(description='protein_synthesis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float46 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate at mRNA creates complete set of proteins', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float46, units_btn, description_btn] box52 = Box(children=row, layout=box_layout) name_btn = Button(description='virion_assembly_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float47 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='rate at which viral proteins are assembled into complete virion', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float47, units_btn, description_btn] box53 = Box(children=row, layout=box_layout) name_btn = Button(description='virion_export_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float48 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate at which a virion is exported from a live cell', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float48, units_btn, description_btn] box54 = Box(children=row, layout=box_layout) name_btn = Button(description='unbound_external_ACE2', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float49 = FloatText(value='1000', step='100', style=style, layout=widget_layout) units_btn = Button(description='receptors', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='initial number of unbound ACE2 receptors on surface', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float49, units_btn, description_btn] box55 = Box(children=row, layout=box_layout) name_btn = Button(description='bound_external_ACE2', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float50 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='receptors', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='initial number of bound ACE2 receptors on surface', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float50, units_btn, description_btn] box56 = Box(children=row, layout=box_layout) name_btn = Button(description='unbound_internal_ACE2', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float51 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='receptors', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='initial number of internalized unbound ACE2 receptors', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float51, units_btn, description_btn] box57 = Box(children=row, layout=box_layout) name_btn = Button(description='bound_internal_ACE2', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float52 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='receptors', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='initial number of internalized bound ACE2 receptors', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float52, units_btn, description_btn] box58 = Box(children=row, layout=box_layout) name_btn = Button(description='ACE2_binding_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float53 = FloatText(value='0.001', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='ACE2 receptor-virus binding rate', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float53, units_btn, description_btn] box59 = Box(children=row, layout=box_layout) name_btn = Button(description='ACE2_endocytosis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float54 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='ACE2 receptor-virus endocytosis rate', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float54, units_btn, description_btn] box60 = Box(children=row, layout=box_layout) name_btn = Button(description='ACE2_cargo_release_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float55 = FloatText(value='0.001', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='ACE2 receptor-virus cargo release rate', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float55, units_btn, description_btn] box61 = Box(children=row, layout=box_layout) name_btn = Button(description='ACE2_recycling_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float56 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='ACE2 receptor recycling rate', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float56, units_btn, description_btn] box62 = Box(children=row, layout=box_layout) name_btn = Button(description='max_infected_apoptosis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float57 = FloatText(value='0.001', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='maximum rate of cell apoptosis due to viral infection', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float57, units_btn, description_btn] box63 = Box(children=row, layout=box_layout) name_btn = Button(description='max_apoptosis_half_max', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float58 = FloatText(value='250', step='10', style=style, layout=widget_layout) units_btn = Button(description='virion', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='viral load at which cells reach half max apoptosis rate', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float58, units_btn, description_btn] box64 = Box(children=row, layout=box_layout) name_btn = Button(description='apoptosis_hill_power', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float59 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='none', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='Hill power for viral load apoptosis response', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float59, units_btn, description_btn] box65 = Box(children=row, layout=box_layout) name_btn = Button(description='virus_fraction_released_at_death', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float60 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='none', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='fraction of internal virus released at cell death', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float60, units_btn, description_btn] box66 = Box(children=row, layout=box_layout) name_btn = Button(description='infected_cell_chemokine_secretion_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float61 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='max rate that infected cells secrete chemokine', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float61, units_btn, description_btn] box67 = Box(children=row, layout=box_layout) name_btn = Button(description='debris_secretion_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float62 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate that dead cells release debris', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float62, units_btn, description_btn] box68 = Box(children=row, layout=box_layout) name_btn = Button(description='infected_cell_chemokine_secretion_activated', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float63 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='none', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='used internally to track activation of chemokine secretion', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float63, units_btn, description_btn] box69 = Box(children=row, layout=box_layout) name_btn = Button(description='TCell_contact_time', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float64 = FloatText(value='0.0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='tracks total contact time with CD8 T cells', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float64, units_btn, description_btn] box70 = Box(children=row, layout=box_layout) name_btn = Button(description='cell_attachment_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float65 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='the rate at which the cell attaches to cells in contact', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float65, units_btn, description_btn] box71 = Box(children=row, layout=box_layout) name_btn = Button(description='cell_attachment_lifetime', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float66 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='the mean duration of a cell-cell attachment', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float66, units_btn, description_btn] box72 = Box(children=row, layout=box_layout) name_btn = Button(description='TCell_contact_death_threshold', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float67 = FloatText(value='50', step='1', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='threshold CD8 T cell contact time to trigger apoptosis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float67, units_btn, description_btn] box73 = Box(children=row, layout=box_layout) name_btn = Button(description='max_attachment_distance', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float68 = FloatText(value='15', step='1', style=style, layout=widget_layout) units_btn = Button(description='micron', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float68, units_btn, description_btn] box74 = Box(children=row, layout=box_layout) name_btn = Button(description='elastic_attachment_coefficient', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float69 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='elastic coefficient for cell-cell attachment', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float69, units_btn, description_btn] box75 = Box(children=row, layout=box_layout) name_btn = Button(description='phagocytosis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float70 = FloatText(value='0.167', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float70, units_btn, description_btn] box76 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_debris_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float71 = FloatText(value='1.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='relative sensitivity to debris in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float71, units_btn, description_btn] box77 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_chemokine_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float72 = FloatText(value='10.0', step='1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='relative sensitivity to chemokine in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float72, units_btn, description_btn] box78 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float73 = FloatText(value='0.4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='speed after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float73, units_btn, description_btn] box79 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_cytokine_secretion_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float74 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate of secreting pro-inflamatory cytokine after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float74, units_btn, description_btn] box80 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_immune_cell', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float75 = FloatText(value='0.0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='used internally to track activation state', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float75, units_btn, description_btn] box81 = Box(children=row, layout=box_layout) name_btn = Button(description='virus_expression_threshold', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float76 = FloatText(value='10.0', step='1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='minimal quantity of virus to activate virus_expression node', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float76, units_btn, description_btn] box82 = Box(children=row, layout=box_layout) self.cell_def_vbox0 = VBox([ div_row1, box0, box1, box2, box3, div_row2, death_model1,box4, box5, box6, box7, box8, box9, box10, death_model2,box11, box12, box13, box14, box15, box16, box17, div_row3, box18, box19, box20, box21, box22, box23, box24, box25, box26, div_row4, box27, box28, box29, box30, box31, div_row5, box32,box33,box34,self.bool2,self.bool3,chemotaxis_btn,self.bool4,box35,box36,div_row6, box37,box38,box39,box40,box41,box42,box43,box44,div_row7, div_row8, box45, box46, box47, box48, box49, box50, box51, box52, box53, box54, box55, box56, box57, box58, box59, box60, box61, box62, box63, box64, box65, box66, box67, box68, box69, box70, box71, box72, box73, box74, box75, box76, box77, box78, box79, box80, box81, box82, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox0) # >>>>>>>>>>>>>>>>> = lung epithelium # ------------------------- div_row9 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row9.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float77 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float77, units_btn, ] box83 = Box(children=row, layout=box_layout) # ------------------------- div_row10 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row10.style.button_color = 'orange' self.bool5 = Checkbox(description='enabled', value=False,layout=name_button_layout) # ------------------------- div_row11 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout) div_row11.style.button_color = 'orange' # ------------------------- div_row12 = Button(description='phenotype:intracellular (maboss)', disabled=True, layout=divider_button_layout) div_row12.style.button_color = 'orange' bnd_filename = Button(description='bnd_filename', disabled=True, layout=name_button_layout) bnd_filename.style.button_color = 'lightgreen' self.bnd_filenames[1] = Text(value='../data/boolean_network/epithelial_cell_2.bnd', style=style, layout=widget_layout) row = [bnd_filename, self.bnd_filenames[1]] box84 = Box(children=row, layout=box_layout) cfg_filename = Button(description='cfg_filename', disabled=True, layout=name_button_layout) cfg_filename.style.button_color = 'tan' self.cfg_filenames[1] = Text(value='../data/boolean_network/epithelial_cell_2.cfg', style=style, layout=widget_layout) row = [cfg_filename, self.cfg_filenames[1]] box85 = Box(children=row, layout=box_layout) time_step = Button(description='time_step', disabled=True, layout=name_button_layout) time_step.style.button_color = 'lightgreen' self.float78 = FloatText(value='12', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [time_step, self.float78, units_btn] box86 = Box(children=row, layout=box_layout) # ================== , if present ================== self.cell_def_vbox1 = VBox([ div_row9, death_model1,box83, div_row10, self.bool5,div_row11, div_row12, box84,box85,box86, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox1) # >>>>>>>>>>>>>>>>> = immune # ------------------------- div_row13 = Button(description='phenotype:mechanics', disabled=True, layout=divider_button_layout) div_row13.style.button_color = 'orange' name_btn = Button(description='cell_cell_adhesion_strength', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float79 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' time_step = [name_btn, self.float79, units_btn, ] box87 = Box(children=time_step, layout=box_layout) name_btn = Button(description='cell_cell_repulsion_strength', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float80 = FloatText(value='10', step='1', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' time_step = [name_btn, self.float80, units_btn, ] box88 = Box(children=time_step, layout=box_layout) # ------------------------- div_row14 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row14.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float81 = FloatText(value='5e-4', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' time_step = [name_btn, self.float81, units_btn, ] box89 = Box(children=time_step, layout=box_layout) # ------------------------- div_row15 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row15.style.button_color = 'orange' name_btn = Button(description='speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float82 = FloatText(value='4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float82, units_btn] box90 = Box(children=row, layout=box_layout) name_btn = Button(description='persistence_time', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float83 = FloatText(value='5', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float83, units_btn] box91 = Box(children=row, layout=box_layout) name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float84 = FloatText(value='0.70', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float84, units_btn] box92 = Box(children=row, layout=box_layout) self.bool6 = Checkbox(description='enabled', value=True,layout=name_button_layout) self.bool7 = Checkbox(description='use_2D', value=True,layout=name_button_layout) chemotaxis_btn = Button(description='chemotaxis', disabled=True, layout={'width':'30%'}) chemotaxis_btn.style.button_color = '#ffde6b' self.bool8 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.chemotaxis_substrate3 = Text(value='chemokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_substrate3] box93 = Box(children=row, layout=box_layout) name_btn = Button(description='direction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.chemotaxis_direction3 = Text(value='1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_direction3] box94 = Box(children=row, layout=box_layout) # ------------------------- div_row16 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout) div_row16.style.button_color = 'orange' name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text4 = Text(value='pro-inflammatory cytokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text4] box95 = Box(children=row, layout=box_layout) name_btn = Button(description='uptake_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float85 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float85, units_btn] box96 = Box(children=row, layout=box_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text5 = Text(value='chemokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text5] box97 = Box(children=row, layout=box_layout) name_btn = Button(description='uptake_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float86 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float86, units_btn] box98 = Box(children=row, layout=box_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text6 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text6] box99 = Box(children=row, layout=box_layout) name_btn = Button(description='uptake_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float87 = FloatText(value='0.1', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float87, units_btn] box100 = Box(children=row, layout=box_layout) # ================== , if present ================== self.cell_def_vbox2 = VBox([ div_row13, box87, box88, div_row14, death_model1,box89, div_row15, box90,box91,box92,self.bool6,self.bool7,chemotaxis_btn,self.bool8,box93,box94,div_row16, box95,box96,box97,box98,box99,box100, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox2) # >>>>>>>>>>>>>>>>> = CD8 Tcell # ------------------------- div_row17 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row17.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float88 = FloatText(value='2.8e-4', step='1e-05', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' time_step = [name_btn, self.float88, units_btn, ] box101 = Box(children=time_step, layout=box_layout) # ------------------------- div_row18 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row18.style.button_color = 'orange' name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float89 = FloatText(value='0.70', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float89, units_btn] box102 = Box(children=row, layout=box_layout) self.bool9 = Checkbox(description='enabled', value=True,layout=name_button_layout) self.bool10 = Checkbox(description='use_2D', value=True,layout=name_button_layout) chemotaxis_btn = Button(description='chemotaxis', disabled=True, layout={'width':'30%'}) chemotaxis_btn.style.button_color = '#ffde6b' self.bool11 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.chemotaxis_substrate4 = Text(value='chemokine', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_substrate4] box103 = Box(children=row, layout=box_layout) name_btn = Button(description='direction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.chemotaxis_direction4 = Text(value='1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_direction4] box104 = Box(children=row, layout=box_layout) # ------------------------- div_row19 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout) div_row19.style.button_color = 'orange' name_btn = Button(description='total', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float90 = FloatText(value='478', step='10', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' time_step = [name_btn, self.float90, units_btn, ] box105 = Box(children=time_step, layout=box_layout) name_btn = Button(description='nuclear', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float91 = FloatText(value='47.8', step='1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' time_step = [name_btn, self.float91, units_btn, ] box106 = Box(children=time_step, layout=box_layout) # ------------------------- div_row20 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout) div_row20.style.button_color = 'orange' name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.text7 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text7] box107 = Box(children=row, layout=box_layout) name_btn = Button(description='uptake_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float92 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float92, units_btn] box108 = Box(children=row, layout=box_layout) # ------------------------- div_row21 = Button(description='phenotype:intracellular (maboss)', disabled=True, layout=divider_button_layout) div_row21.style.button_color = 'orange' bnd_filename = Button(description='bnd_filename', disabled=True, layout=name_button_layout) bnd_filename.style.button_color = 'tan' self.bnd_filenames[3] = Text(value='../data/boolean_network/cd8t_cell.bnd', style=style, layout=widget_layout) row = [bnd_filename, self.bnd_filenames[3]] box109 = Box(children=row, layout=box_layout) cfg_filename = Button(description='cfg_filename', disabled=True, layout=name_button_layout) cfg_filename.style.button_color = 'lightgreen' self.cfg_filenames[3] = Text(value='../data/boolean_network/cd8t_cell.cfg', style=style, layout=widget_layout) row = [cfg_filename, self.cfg_filenames[3]] box110 = Box(children=row, layout=box_layout) time_step = Button(description='time_step', disabled=True, layout=name_button_layout) time_step.style.button_color = 'tan' self.float93 = FloatText(value='12', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [time_step, self.float93, units_btn] box111 = Box(children=row, layout=box_layout) # ================== , if present ================== div_row22 = Button(description='Custom Data',disabled=True, layout=divider_button_layout) div_row22.style.button_color = 'cyan' name_btn = Button(description='cell_attachment_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float94 = FloatText(value='0.2', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float94, units_btn, description_btn] box112 = Box(children=row, layout=box_layout) name_btn = Button(description='cell_attachment_lifetime', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float95 = FloatText(value='8.5', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float95, units_btn, description_btn] box113 = Box(children=row, layout=box_layout) self.cell_def_vbox3 = VBox([ div_row17, death_model1,box101, div_row18, box102,self.bool9,self.bool10,chemotaxis_btn,self.bool11,box103,box104,div_row19, box105, box106, div_row20, box107,box108,div_row21, box109,box110,box111,div_row22, box112, box113, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox3) # >>>>>>>>>>>>>>>>> = macrophage # ------------------------- div_row23 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row23.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float96 = FloatText(value='2.1e-4', step='1e-05', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float96, units_btn, ] box114 = Box(children=row, layout=box_layout) # ------------------------- div_row24 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row24.style.button_color = 'orange' name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float97 = FloatText(value='0.7', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float97, units_btn] box115 = Box(children=row, layout=box_layout) name_btn = Button(description='persistence_time', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float98 = FloatText(value='5', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float98, units_btn] box116 = Box(children=row, layout=box_layout) self.bool12 = Checkbox(description='enabled', value=True,layout=name_button_layout) self.bool13 = Checkbox(description='use_2D', value=True,layout=name_button_layout) chemotaxis_btn = Button(description='chemotaxis', disabled=True, layout={'width':'30%'}) chemotaxis_btn.style.button_color = '#ffde6b' self.bool14 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.chemotaxis_substrate5 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_substrate5] box117 = Box(children=row, layout=box_layout) name_btn = Button(description='direction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.chemotaxis_direction5 = Text(value='1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_direction5] box118 = Box(children=row, layout=box_layout) # ------------------------- div_row25 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout) div_row25.style.button_color = 'orange' name_btn = Button(description='total', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float99 = FloatText(value='4849', step='100', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float99, units_btn, ] box119 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float100 = FloatText(value='485', step='10', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float100, units_btn, ] box120 = Box(children=row, layout=box_layout) name_btn = Button(description='cytoplasmic_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float101 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float101, units_btn, ] box121 = Box(children=row, layout=box_layout) # ------------------------- div_row26 = Button(description='phenotype:intracellular (maboss)', disabled=True, layout=divider_button_layout) div_row26.style.button_color = 'orange' bnd_filename = Button(description='bnd_filename', disabled=True, layout=name_button_layout) bnd_filename.style.button_color = 'lightgreen' self.bnd_filenames[4] = Text(value='../data/boolean_network/macrophage.bnd', style=style, layout=widget_layout) row = [bnd_filename, self.bnd_filenames[4]] box122 = Box(children=row, layout=box_layout) cfg_filename = Button(description='cfg_filename', disabled=True, layout=name_button_layout) cfg_filename.style.button_color = 'tan' self.cfg_filenames[4] = Text(value='../data/boolean_network/macrophage.cfg', style=style, layout=widget_layout) row = [cfg_filename, self.cfg_filenames[4]] box123 = Box(children=row, layout=box_layout) time_step = Button(description='time_step', disabled=True, layout=name_button_layout) time_step.style.button_color = 'lightgreen' self.float102 = FloatText(value='12', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [time_step, self.float102, units_btn] box124 = Box(children=row, layout=box_layout) # ================== , if present ================== div_row27 = Button(description='Custom Data',disabled=True, layout=divider_button_layout) div_row27.style.button_color = 'cyan' name_btn = Button(description='phagocytosis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float103 = FloatText(value='0.167', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float103, units_btn, description_btn] box125 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_debris_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float104 = FloatText(value='1.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='relative sensitivity to debris in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float104, units_btn, description_btn] box126 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_chemokine_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float105 = FloatText(value='10.0', step='1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='relative sensitivity to chemokine in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float105, units_btn, description_btn] box127 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float106 = FloatText(value='0.4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='speed after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float106, units_btn, description_btn] box128 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_cytokine_secretion_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float107 = FloatText(value='1', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='rate of secreting pro-inflamatory cytokine after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float107, units_btn, description_btn] box129 = Box(children=row, layout=box_layout) self.cell_def_vbox4 = VBox([ div_row23, death_model1,box114, div_row24, box115,box116,self.bool12,self.bool13,chemotaxis_btn,self.bool14,box117,box118,div_row25, box119, box120, box121, div_row26, box122,box123,box124,div_row27, box125, box126, box127, box128, box129, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox4) # >>>>>>>>>>>>>>>>> = neutrophil # ------------------------- div_row28 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout) div_row28.style.button_color = 'orange' death_model1 = Button(description='model: apoptosis', disabled=True, layout={'width':'30%'}) death_model1.style.button_color = '#ffde6b' name_btn = Button(description='death rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float108 = FloatText(value='8.9e-4', step='0.0001', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float108, units_btn, ] box130 = Box(children=row, layout=box_layout) # ------------------------- div_row29 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout) div_row29.style.button_color = 'orange' name_btn = Button(description='speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float109 = FloatText(value='19', step='1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float109, units_btn] box131 = Box(children=row, layout=box_layout) name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float110 = FloatText(value='0.91', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float110, units_btn] box132 = Box(children=row, layout=box_layout) name_btn = Button(description='persistence_time', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float111 = FloatText(value='5', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float111, units_btn] box133 = Box(children=row, layout=box_layout) self.bool15 = Checkbox(description='enabled', value=True,layout=name_button_layout) self.bool16 = Checkbox(description='use_2D', value=True,layout=name_button_layout) chemotaxis_btn = Button(description='chemotaxis', disabled=True, layout={'width':'30%'}) chemotaxis_btn.style.button_color = '#ffde6b' self.bool17 = Checkbox(description='enabled', value=False,layout=name_button_layout) name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.chemotaxis_substrate6 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_substrate6] box134 = Box(children=row, layout=box_layout) name_btn = Button(description='direction', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.chemotaxis_direction6 = Text(value='1', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.chemotaxis_direction6] box135 = Box(children=row, layout=box_layout) # ------------------------- div_row30 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout) div_row30.style.button_color = 'orange' name_btn = Button(description='substrate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.text8 = Text(value='virion', disabled=False, style=style, layout=widget_layout_long) row = [name_btn, self.text8] box136 = Box(children=row, layout=box_layout) name_btn = Button(description='uptake_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float112 = FloatText(value='0.1', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float112, units_btn] box137 = Box(children=row, layout=box_layout) # ------------------------- div_row31 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout) div_row31.style.button_color = 'orange' name_btn = Button(description='total', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float113 = FloatText(value='1437', step='100', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float113, units_btn, ] box138 = Box(children=row, layout=box_layout) name_btn = Button(description='nuclear', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float114 = FloatText(value='143.7', step='10', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' row = [name_btn, self.float114, units_btn, ] box139 = Box(children=row, layout=box_layout) name_btn = Button(description='cytoplasmic_biomass_change_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float115 = FloatText(value='0.045', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [name_btn, self.float115, units_btn, ] box140 = Box(children=row, layout=box_layout) # ------------------------- div_row32 = Button(description='phenotype:intracellular (maboss)', disabled=True, layout=divider_button_layout) div_row32.style.button_color = 'orange' bnd_filename = Button(description='bnd_filename', disabled=True, layout=name_button_layout) bnd_filename.style.button_color = 'tan' self.bnd_filenames[5] = Text(value='../data/boolean_network/neutrophil.bnd', style=style, layout=widget_layout) row = [bnd_filename, self.bnd_filenames[5]] box141 = Box(children=row, layout=box_layout) cfg_filename = Button(description='cfg_filename', disabled=True, layout=name_button_layout) cfg_filename.style.button_color = 'lightgreen' self.cfg_filenames[5] = Text(value='../data/boolean_network/neutrophil.cfg', style=style, layout=widget_layout) row = [cfg_filename, self.cfg_filenames[5]] box142 = Box(children=row, layout=box_layout) time_step = Button(description='time_step', disabled=True, layout=name_button_layout) time_step.style.button_color = 'tan' self.float116 = FloatText(value='12', style=style, layout=widget_layout) units_btn = Button(description='min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' row = [time_step, self.float116, units_btn] box143 = Box(children=row, layout=box_layout) # ================== , if present ================== div_row33 = Button(description='Custom Data',disabled=True, layout=divider_button_layout) div_row33.style.button_color = 'cyan' name_btn = Button(description='phagocytosis_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float117 = FloatText(value='0.117', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float117, units_btn, description_btn] box144 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_debris_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float118 = FloatText(value='1.0', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='relative sensitivity to debris in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float118, units_btn, description_btn] box145 = Box(children=row, layout=box_layout) name_btn = Button(description='sensitivity_to_chemokine_chemotaxis', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float119 = FloatText(value='10.0', step='1', style=style, layout=widget_layout) units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='relative sensitivity to chemokine in chemotaxis', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float119, units_btn, description_btn] box146 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_speed', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'tan' self.float120 = FloatText(value='0.4', step='0.1', style=style, layout=widget_layout) units_btn = Button(description='micron/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'tan' description_btn = Button(description='speed after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'tan' row = [name_btn, self.float120, units_btn, description_btn] box147 = Box(children=row, layout=box_layout) name_btn = Button(description='activated_cytokine_secretion_rate', disabled=True, layout=name_button_layout) name_btn.style.button_color = 'lightgreen' self.float121 = FloatText(value='0', step='0.01', style=style, layout=widget_layout) units_btn = Button(description='1/min', disabled=True, layout=name_button_layout) units_btn.style.button_color = 'lightgreen' description_btn = Button(description='rate of secreting pro-inflamatory cytokine after activation', disabled=True, layout=desc_button_layout) description_btn.style.button_color = 'lightgreen' row = [name_btn, self.float121, units_btn, description_btn] box148 = Box(children=row, layout=box_layout) self.cell_def_vbox5 = VBox([ div_row28, death_model1,box130, div_row29, box131,box132,box133,self.bool15,self.bool16,chemotaxis_btn,self.bool17,box134,box135,div_row30, box136,box137,div_row31, box138, box139, box140, div_row32, box141,box142,box143,div_row33, box144, box145, box146, box147, box148, ]) # ------------------------------------------ self.cell_def_vboxes.append(self.cell_def_vbox5) row = [name_btn, self.float121, units_btn, description_btn] box143 = Box(children=row, layout=box_layout) self.tab = VBox([ self.cell_type_parent_row, explain_inheritance, self.cell_def_vbox0, self.cell_def_vbox1, self.cell_def_vbox2, self.cell_def_vbox3, self.cell_def_vbox4, self.cell_def_vbox5, ]) self.display_cell_type_default() #------------------------------ def cell_type_cb(self, change): if change['type'] == 'change' and change['name'] == 'value': # print("changed to %s" % change['new']) self.parent_name.value = self.cell_type_parent_dict[change['new']] idx_selected = list(self.cell_type_parent_dict.keys()).index(change['new']) # print('index=',idx_selected) # self.vbox1.layout.visibility = 'hidden' # vs. visible # self.vbox1.layout.visibility = None # There's probably a better way to do this, but for now, # we hide all vboxes containing the widgets for the different cell defs # and only display the contents of the selected one. for vb in self.cell_def_vboxes: vb.layout.display = 'none' # vs. 'contents' self.cell_def_vboxes[idx_selected].layout.display = 'contents' # vs. 'contents' #------------------------------ def display_cell_type_default(self): # print("display_cell_type_default():") #print(" self.cell_type_parent_dict = ",self.cell_type_parent_dict) # There's probably a better way to do this, but for now, # we hide all vboxes containing the widgets for the different cell defs # and only display the contents of 'default' for vb in self.cell_def_vboxes: vb.layout.display = 'none' # vs. 'contents' self.cell_def_vboxes[0].layout.display = 'contents' # Populate the GUI widgets with values from the XML def fill_gui(self, xml_root): uep = xml_root.find('.//cell_definitions') # find unique entry point # ------------------ cell_definition: default # --------- cycle (flow_cytometry_separated_cycle_model) self.float0.value = float(uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[1]').text) self.float1.value = float(uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[2]').text) self.float2.value = float(uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[3]').text) self.float3.value = float(uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[4]').text) # --------- death self.float4.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//death_rate').text) self.float5.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//unlysed_fluid_change_rate').text) self.float6.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//lysed_fluid_change_rate').text) self.float7.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//cytoplasmic_biomass_change_rate').text) self.float8.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//nuclear_biomass_change_rate').text) self.float9.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//calcification_rate').text) self.float10.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//relative_rupture_volume').text) self.float11.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//death_rate').text) self.float12.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//unlysed_fluid_change_rate').text) self.float13.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//lysed_fluid_change_rate').text) self.float14.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//cytoplasmic_biomass_change_rate').text) self.float15.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//nuclear_biomass_change_rate').text) self.float16.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//calcification_rate').text) self.float17.value = float(uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//relative_rupture_volume').text) # --------- volume self.float18.value = float(uep.find('.//cell_definition[1]//phenotype//volume//total').text) self.float19.value = float(uep.find('.//cell_definition[1]//phenotype//volume//fluid_fraction').text) self.float20.value = float(uep.find('.//cell_definition[1]//phenotype//volume//nuclear').text) self.float21.value = float(uep.find('.//cell_definition[1]//phenotype//volume//fluid_change_rate').text) self.float22.value = float(uep.find('.//cell_definition[1]//phenotype//volume//cytoplasmic_biomass_change_rate').text) self.float23.value = float(uep.find('.//cell_definition[1]//phenotype//volume//nuclear_biomass_change_rate').text) self.float24.value = float(uep.find('.//cell_definition[1]//phenotype//volume//calcified_fraction').text) self.float25.value = float(uep.find('.//cell_definition[1]//phenotype//volume//calcification_rate').text) self.float26.value = float(uep.find('.//cell_definition[1]//phenotype//volume//relative_rupture_volume').text) # --------- mechanics self.float27.value = float(uep.find('.//cell_definition[1]//phenotype//mechanics//cell_cell_adhesion_strength').text) self.float28.value = float(uep.find('.//cell_definition[1]//phenotype//mechanics//cell_cell_repulsion_strength').text) self.float29.value = float(uep.find('.//cell_definition[1]//phenotype//mechanics//relative_maximum_adhesion_distance').text) self.bool0.value = ('true' == (uep.find('.//cell_definition[1]//phenotype//mechanics//options//set_relative_equilibrium_distance').attrib['enabled'].lower())) self.bool1.value = ('true' == (uep.find('.//cell_definition[1]//phenotype//mechanics//options//set_absolute_equilibrium_distance').attrib['enabled'].lower())) # --------- motility self.float32.value = float(uep.find('.//cell_definition[1]//phenotype//motility//speed').text) self.float33.value = float(uep.find('.//cell_definition[1]//phenotype//motility//persistence_time').text) self.float34.value = float(uep.find('.//cell_definition[1]//phenotype//motility//migration_bias').text) self.bool2.value = ('true' == (uep.find('.//cell_definition[1]//phenotype//motility//options//enabled').text.lower())) self.bool3.value = ('true' == (uep.find('.//cell_definition[1]//phenotype//motility//options//use_2D').text.lower())) self.bool4.value = ('true' == (uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//enabled').text.lower())) self.chemotaxis_substrate1.value = uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//substrate').text self.chemotaxis_direction1.value = uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//direction').text # --------- secretion self.text0.value = uep.find('.//cell_definition[1]//phenotype//secretion//substrate[1]').attrib['name'] self.float35.value = float(uep.find('.//cell_definition[1]//phenotype//secretion//substrate[1]//secretion_target').text) self.text1.value = uep.find('.//cell_definition[1]//phenotype//secretion//substrate[2]').attrib['name'] self.float36.value = float(uep.find('.//cell_definition[1]//phenotype//secretion//substrate[2]//secretion_target').text) self.text2.value = uep.find('.//cell_definition[1]//phenotype//secretion//substrate[3]').attrib['name'] self.float37.value = float(uep.find('.//cell_definition[1]//phenotype//secretion//substrate[3]//secretion_target').text) self.text3.value = uep.find('.//cell_definition[1]//phenotype//secretion//substrate[4]').attrib['name'] self.float38.value = float(uep.find('.//cell_definition[1]//phenotype//secretion//substrate[4]//secretion_target').text) # --------- molecular # ------------------ cell_definition: lung epithelium # --------- death self.float77.value = float(uep.find('.//cell_definition[2]//phenotype//death//model[1]//death_rate').text) # --------- motility self.bool5.value = ('true' == (uep.find('.//cell_definition[2]//phenotype//motility//options//enabled').text.lower())) # --------- secretion # --------- intracellular self.bnd_filenames[1].value = uep.find('.//cell_definition[2]//phenotype//intracellular//bnd_filename').text self.cfg_filenames[1].value = uep.find('.//cell_definition[2]//phenotype//intracellular//cfg_filename').text self.float78.value = float(uep.find('.//cell_definition[2]//phenotype//intracellular//time_step').text) # ------------------ cell_definition: immune # --------- mechanics self.float79.value = float(uep.find('.//cell_definition[3]//phenotype//mechanics//cell_cell_adhesion_strength').text) self.float80.value = float(uep.find('.//cell_definition[3]//phenotype//mechanics//cell_cell_repulsion_strength').text) # --------- death self.float81.value = float(uep.find('.//cell_definition[3]//phenotype//death//model[1]//death_rate').text) # --------- motility self.float82.value = float(uep.find('.//cell_definition[3]//phenotype//motility//speed').text) self.float83.value = float(uep.find('.//cell_definition[3]//phenotype//motility//persistence_time').text) self.float84.value = float(uep.find('.//cell_definition[3]//phenotype//motility//migration_bias').text) self.bool6.value = ('true' == (uep.find('.//cell_definition[3]//phenotype//motility//options//enabled').text.lower())) self.bool7.value = ('true' == (uep.find('.//cell_definition[3]//phenotype//motility//options//use_2D').text.lower())) self.bool8.value = ('true' == (uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//enabled').text.lower())) self.chemotaxis_substrate3.value = uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//substrate').text self.chemotaxis_direction3.value = uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//direction').text # --------- secretion self.text4.value = uep.find('.//cell_definition[3]//phenotype//secretion//substrate[1]').attrib['name'] self.float85.value = float(uep.find('.//cell_definition[3]//phenotype//secretion//substrate[1]//uptake_rate').text) self.text5.value = uep.find('.//cell_definition[3]//phenotype//secretion//substrate[2]').attrib['name'] self.float86.value = float(uep.find('.//cell_definition[3]//phenotype//secretion//substrate[2]//uptake_rate').text) self.text6.value = uep.find('.//cell_definition[3]//phenotype//secretion//substrate[3]').attrib['name'] self.float87.value = float(uep.find('.//cell_definition[3]//phenotype//secretion//substrate[3]//uptake_rate').text) # ------------------ cell_definition: CD8 Tcell # --------- death self.float88.value = float(uep.find('.//cell_definition[4]//phenotype//death//model[1]//death_rate').text) # --------- motility self.float89.value = float(uep.find('.//cell_definition[4]//phenotype//motility//migration_bias').text) self.bool9.value = ('true' == (uep.find('.//cell_definition[4]//phenotype//motility//options//enabled').text.lower())) self.bool10.value = ('true' == (uep.find('.//cell_definition[4]//phenotype//motility//options//use_2D').text.lower())) self.bool11.value = ('true' == (uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//enabled').text.lower())) self.chemotaxis_substrate4.value = uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//substrate').text self.chemotaxis_direction4.value = uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//direction').text # --------- volume self.float90.value = float(uep.find('.//cell_definition[4]//phenotype//volume//total').text) self.float91.value = float(uep.find('.//cell_definition[4]//phenotype//volume//nuclear').text) # --------- secretion self.text7.value = uep.find('.//cell_definition[4]//phenotype//secretion//substrate[1]').attrib['name'] self.float92.value = float(uep.find('.//cell_definition[4]//phenotype//secretion//substrate[1]//uptake_rate').text) # --------- intracellular self.bnd_filenames[3].value = uep.find('.//cell_definition[4]//phenotype//intracellular//bnd_filename').text self.cfg_filenames[3].value = uep.find('.//cell_definition[4]//phenotype//intracellular//cfg_filename').text self.float93.value = float(uep.find('.//cell_definition[4]//phenotype//intracellular//time_step').text) # ------------------ cell_definition: macrophage # --------- death self.float96.value = float(uep.find('.//cell_definition[5]//phenotype//death//model[1]//death_rate').text) # --------- motility self.float97.value = float(uep.find('.//cell_definition[5]//phenotype//motility//migration_bias').text) self.float98.value = float(uep.find('.//cell_definition[5]//phenotype//motility//persistence_time').text) self.bool12.value = ('true' == (uep.find('.//cell_definition[5]//phenotype//motility//options//enabled').text.lower())) self.bool13.value = ('true' == (uep.find('.//cell_definition[5]//phenotype//motility//options//use_2D').text.lower())) self.bool14.value = ('true' == (uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//enabled').text.lower())) self.chemotaxis_substrate5.value = uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//substrate').text self.chemotaxis_direction5.value = uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//direction').text # --------- volume self.float99.value = float(uep.find('.//cell_definition[5]//phenotype//volume//total').text) self.float100.value = float(uep.find('.//cell_definition[5]//phenotype//volume//nuclear').text) self.float101.value = float(uep.find('.//cell_definition[5]//phenotype//volume//cytoplasmic_biomass_change_rate').text) # --------- intracellular self.bnd_filenames[4].value = uep.find('.//cell_definition[5]//phenotype//intracellular//bnd_filename').text self.cfg_filenames[4].value = uep.find('.//cell_definition[5]//phenotype//intracellular//cfg_filename').text self.float102.value = float(uep.find('.//cell_definition[5]//phenotype//intracellular//time_step').text) # ------------------ cell_definition: neutrophil # --------- death self.float108.value = float(uep.find('.//cell_definition[6]//phenotype//death//model[1]//death_rate').text) # --------- motility self.float109.value = float(uep.find('.//cell_definition[6]//phenotype//motility//speed').text) self.float110.value = float(uep.find('.//cell_definition[6]//phenotype//motility//migration_bias').text) self.float111.value = float(uep.find('.//cell_definition[6]//phenotype//motility//persistence_time').text) self.bool15.value = ('true' == (uep.find('.//cell_definition[6]//phenotype//motility//options//enabled').text.lower())) self.bool16.value = ('true' == (uep.find('.//cell_definition[6]//phenotype//motility//options//use_2D').text.lower())) self.bool17.value = ('true' == (uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//enabled').text.lower())) self.chemotaxis_substrate6.value = uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//substrate').text self.chemotaxis_direction6.value = uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//direction').text # --------- secretion self.text8.value = uep.find('.//cell_definition[6]//phenotype//secretion//substrate[1]').attrib['name'] self.float112.value = float(uep.find('.//cell_definition[6]//phenotype//secretion//substrate[1]//uptake_rate').text) # --------- volume self.float113.value = float(uep.find('.//cell_definition[6]//phenotype//volume//total').text) self.float114.value = float(uep.find('.//cell_definition[6]//phenotype//volume//nuclear').text) self.float115.value = float(uep.find('.//cell_definition[6]//phenotype//volume//cytoplasmic_biomass_change_rate').text) # --------- intracellular self.bnd_filenames[5].value = uep.find('.//cell_definition[6]//phenotype//intracellular//bnd_filename').text self.cfg_filenames[5].value = uep.find('.//cell_definition[6]//phenotype//intracellular//cfg_filename').text self.float116.value = float(uep.find('.//cell_definition[6]//phenotype//intracellular//time_step').text) # Read values from the GUI widgets to enable editing XML def fill_xml(self, xml_root): uep = xml_root.find('.//cell_definitions') # find unique entry point # ------------------ cell_definition: default # --------- cycle (flow_cytometry_separated_cycle_model) uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[1]').text = str(self.float0.value) uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[2]').text = str(self.float1.value) uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[3]').text = str(self.float2.value) uep.find('.//cell_definition[1]//phenotype//cycle//phase_transition_rates//rate[4]').text = str(self.float3.value) # --------- death uep.find('.//cell_definition[1]//phenotype//death//model[1]//death_rate').text = str(self.float4.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//unlysed_fluid_change_rate').text = str(self.float5.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//lysed_fluid_change_rate').text = str(self.float6.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//cytoplasmic_biomass_change_rate').text = str(self.float7.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//nuclear_biomass_change_rate').text = str(self.float8.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//calcification_rate').text = str(self.float9.value) uep.find('.//cell_definition[1]//phenotype//death//model[1]//parameters//relative_rupture_volume').text = str(self.float10.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//death_rate').text = str(self.float11.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//unlysed_fluid_change_rate').text = str(self.float12.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//lysed_fluid_change_rate').text = str(self.float13.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//cytoplasmic_biomass_change_rate').text = str(self.float14.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//nuclear_biomass_change_rate').text = str(self.float15.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//calcification_rate').text = str(self.float16.value) uep.find('.//cell_definition[1]//phenotype//death//model[2]//parameters//relative_rupture_volume').text = str(self.float17.value) # --------- volume uep.find('.//cell_definition[1]//phenotype//volume//total').text = str(self.float18.value) uep.find('.//cell_definition[1]//phenotype//volume//fluid_fraction').text = str(self.float19.value) uep.find('.//cell_definition[1]//phenotype//volume//nuclear').text = str(self.float20.value) uep.find('.//cell_definition[1]//phenotype//volume//fluid_change_rate').text = str(self.float21.value) uep.find('.//cell_definition[1]//phenotype//volume//cytoplasmic_biomass_change_rate').text = str(self.float22.value) uep.find('.//cell_definition[1]//phenotype//volume//nuclear_biomass_change_rate').text = str(self.float23.value) uep.find('.//cell_definition[1]//phenotype//volume//calcified_fraction').text = str(self.float24.value) uep.find('.//cell_definition[1]//phenotype//volume//calcification_rate').text = str(self.float25.value) uep.find('.//cell_definition[1]//phenotype//volume//relative_rupture_volume').text = str(self.float26.value) # --------- mechanics uep.find('.//cell_definition[1]//phenotype//mechanics//cell_cell_adhesion_strength').text = str(self.float27.value) uep.find('.//cell_definition[1]//phenotype//mechanics//cell_cell_repulsion_strength').text = str(self.float28.value) uep.find('.//cell_definition[1]//phenotype//mechanics//relative_maximum_adhesion_distance').text = str(self.float29.value) uep.find('.//cell_definition[1]//phenotype//mechanics//options//set_relative_equilibrium_distance').attrib['enabled'] = str(self.bool0.value) uep.find('.//cell_definition[1]//phenotype//mechanics//options//set_absolute_equilibrium_distance').attrib['enabled'] = str(self.bool1.value) # --------- motility uep.find('.//cell_definition[1]//phenotype//motility//speed').text = str(self.float32.value) uep.find('.//cell_definition[1]//phenotype//motility//persistence_time').text = str(self.float33.value) uep.find('.//cell_definition[1]//phenotype//motility//migration_bias').text = str(self.float34.value) uep.find('.//cell_definition[1]//phenotype//motility//options//enabled').text = str(self.bool2.value) uep.find('.//cell_definition[1]//phenotype//motility//options//use_2D').text = str(self.bool3.value) uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//enabled').text = str(self.bool4.value) uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//substrate').text = str(self.chemotaxis_substrate1.value) uep.find('.//cell_definition[1]//phenotype//motility//options//chemotaxis//direction').text = str(self.chemotaxis_direction1.value) # --------- secretion uep.find('.//cell_definition[1]//phenotype//secretion//substrate[1]').attrib['name'] = str(self.text0.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[1]//secretion_target').text = str(self.float35.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[2]').attrib['name'] = str(self.text1.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[2]//secretion_target').text = str(self.float36.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[3]').attrib['name'] = str(self.text2.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[3]//secretion_target').text = str(self.float37.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[4]').attrib['name'] = str(self.text3.value) uep.find('.//cell_definition[1]//phenotype//secretion//substrate[4]//secretion_target').text = str(self.float38.value) # --------- molecular # ------------------ cell_definition: lung epithelium # --------- death uep.find('.//cell_definition[2]//phenotype//death//model[1]//death_rate').text = str(self.float77.value) # --------- motility uep.find('.//cell_definition[2]//phenotype//motility//options//enabled').text = str(self.bool5.value) # --------- secretion # --------- intracellular uep.find('.//cell_definition[2]//phenotype//intracellular//bnd_filename').text = str(self.bnd_filenames[1].value) uep.find('.//cell_definition[2]//phenotype//intracellular//cfg_filename').text = str(self.cfg_filenames[1].value) uep.find('.//cell_definition[2]//phenotype//intracellular//time_step').text = str(self.float78.value) # ------------------ cell_definition: immune # --------- mechanics uep.find('.//cell_definition[3]//phenotype//mechanics//cell_cell_adhesion_strength').text = str(self.float79.value) uep.find('.//cell_definition[3]//phenotype//mechanics//cell_cell_repulsion_strength').text = str(self.float80.value) # --------- death uep.find('.//cell_definition[3]//phenotype//death//model[1]//death_rate').text = str(self.float81.value) # --------- motility uep.find('.//cell_definition[3]//phenotype//motility//speed').text = str(self.float82.value) uep.find('.//cell_definition[3]//phenotype//motility//persistence_time').text = str(self.float83.value) uep.find('.//cell_definition[3]//phenotype//motility//migration_bias').text = str(self.float84.value) uep.find('.//cell_definition[3]//phenotype//motility//options//enabled').text = str(self.bool6.value) uep.find('.//cell_definition[3]//phenotype//motility//options//use_2D').text = str(self.bool7.value) uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//enabled').text = str(self.bool8.value) uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//substrate').text = str(self.chemotaxis_substrate3.value) uep.find('.//cell_definition[3]//phenotype//motility//options//chemotaxis//direction').text = str(self.chemotaxis_direction3.value) # --------- secretion uep.find('.//cell_definition[3]//phenotype//secretion//substrate[1]').attrib['name'] = str(self.text4.value) uep.find('.//cell_definition[3]//phenotype//secretion//substrate[1]//uptake_rate').text = str(self.float85.value) uep.find('.//cell_definition[3]//phenotype//secretion//substrate[2]').attrib['name'] = str(self.text5.value) uep.find('.//cell_definition[3]//phenotype//secretion//substrate[2]//uptake_rate').text = str(self.float86.value) uep.find('.//cell_definition[3]//phenotype//secretion//substrate[3]').attrib['name'] = str(self.text6.value) uep.find('.//cell_definition[3]//phenotype//secretion//substrate[3]//uptake_rate').text = str(self.float87.value) # ------------------ cell_definition: CD8 Tcell # --------- death uep.find('.//cell_definition[4]//phenotype//death//model[1]//death_rate').text = str(self.float88.value) # --------- motility uep.find('.//cell_definition[4]//phenotype//motility//migration_bias').text = str(self.float89.value) uep.find('.//cell_definition[4]//phenotype//motility//options//enabled').text = str(self.bool9.value) uep.find('.//cell_definition[4]//phenotype//motility//options//use_2D').text = str(self.bool10.value) uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//enabled').text = str(self.bool11.value) uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//substrate').text = str(self.chemotaxis_substrate4.value) uep.find('.//cell_definition[4]//phenotype//motility//options//chemotaxis//direction').text = str(self.chemotaxis_direction4.value) # --------- volume uep.find('.//cell_definition[4]//phenotype//volume//total').text = str(self.float90.value) uep.find('.//cell_definition[4]//phenotype//volume//nuclear').text = str(self.float91.value) # --------- secretion uep.find('.//cell_definition[4]//phenotype//secretion//substrate[1]').attrib['name'] = str(self.text7.value) uep.find('.//cell_definition[4]//phenotype//secretion//substrate[1]//uptake_rate').text = str(self.float92.value) # --------- intracellular uep.find('.//cell_definition[4]//phenotype//intracellular//bnd_filename').text = str(self.bnd_filenames[3].value) uep.find('.//cell_definition[4]//phenotype//intracellular//cfg_filename').text = str(self.cfg_filenames[3].value) uep.find('.//cell_definition[4]//phenotype//intracellular//time_step').text = str(self.float93.value) # ------------------ cell_definition: macrophage # --------- death uep.find('.//cell_definition[5]//phenotype//death//model[1]//death_rate').text = str(self.float96.value) # --------- motility uep.find('.//cell_definition[5]//phenotype//motility//migration_bias').text = str(self.float97.value) uep.find('.//cell_definition[5]//phenotype//motility//persistence_time').text = str(self.float98.value) uep.find('.//cell_definition[5]//phenotype//motility//options//enabled').text = str(self.bool12.value) uep.find('.//cell_definition[5]//phenotype//motility//options//use_2D').text = str(self.bool13.value) uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//enabled').text = str(self.bool14.value) uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//substrate').text = str(self.chemotaxis_substrate5.value) uep.find('.//cell_definition[5]//phenotype//motility//options//chemotaxis//direction').text = str(self.chemotaxis_direction5.value) # --------- volume uep.find('.//cell_definition[5]//phenotype//volume//total').text = str(self.float99.value) uep.find('.//cell_definition[5]//phenotype//volume//nuclear').text = str(self.float100.value) uep.find('.//cell_definition[5]//phenotype//volume//cytoplasmic_biomass_change_rate').text = str(self.float101.value) # --------- intracellular uep.find('.//cell_definition[5]//phenotype//intracellular//bnd_filename').text = str(self.bnd_filenames[4].value) uep.find('.//cell_definition[5]//phenotype//intracellular//cfg_filename').text = str(self.cfg_filenames[4].value) uep.find('.//cell_definition[5]//phenotype//intracellular//time_step').text = str(self.float102.value) # ------------------ cell_definition: neutrophil # --------- death uep.find('.//cell_definition[6]//phenotype//death//model[1]//death_rate').text = str(self.float108.value) # --------- motility uep.find('.//cell_definition[6]//phenotype//motility//speed').text = str(self.float109.value) uep.find('.//cell_definition[6]//phenotype//motility//migration_bias').text = str(self.float110.value) uep.find('.//cell_definition[6]//phenotype//motility//persistence_time').text = str(self.float111.value) uep.find('.//cell_definition[6]//phenotype//motility//options//enabled').text = str(self.bool15.value) uep.find('.//cell_definition[6]//phenotype//motility//options//use_2D').text = str(self.bool16.value) uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//enabled').text = str(self.bool17.value) uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//substrate').text = str(self.chemotaxis_substrate6.value) uep.find('.//cell_definition[6]//phenotype//motility//options//chemotaxis//direction').text = str(self.chemotaxis_direction6.value) # --------- secretion uep.find('.//cell_definition[6]//phenotype//secretion//substrate[1]').attrib['name'] = str(self.text8.value) uep.find('.//cell_definition[6]//phenotype//secretion//substrate[1]//uptake_rate').text = str(self.float112.value) # --------- volume uep.find('.//cell_definition[6]//phenotype//volume//total').text = str(self.float113.value) uep.find('.//cell_definition[6]//phenotype//volume//nuclear').text = str(self.float114.value) uep.find('.//cell_definition[6]//phenotype//volume//cytoplasmic_biomass_change_rate').text = str(self.float115.value) # --------- intracellular uep.find('.//cell_definition[6]//phenotype//intracellular//bnd_filename').text = str(self.bnd_filenames[5].value) uep.find('.//cell_definition[6]//phenotype//intracellular//cfg_filename').text = str(self.cfg_filenames[5].value) uep.find('.//cell_definition[6]//phenotype//intracellular//time_step').text = str(self.float116.value)