Unverified Commit 1e739ef2 authored by Randy Heiland's avatar Randy Heiland Committed by GitHub
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Merge pull request #4 from pc4covid19/development

Development
parents 6a2f19ee 0a3d038a
# pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app
**Version:** 3.1
**Version:** 3.2
**Release date:** 3 July 2020
**Release date:** 21 July 2020
## Overview
This repository contains code and data for the nanoHUB app https://nanohub.org/tools/pc4covid19.
......@@ -21,6 +21,9 @@ for a summary of changes to the model.
**This model will be continually refined with input from the community, particularly experts in infectious diseases. The validation state will be updated as this progresses.**
## Release summary:
### 3.2:
Updates to the core model; nothing new in the GUI.
### 3.1:
Minor updates to `About` text, e.g., explaining nature of stochastic results. Edits to `immune_submodels.cpp` (see details in the core model repository).
......
......@@ -751,86 +751,66 @@ class CellTypesTab(object):
row = [name_btn, self.float69, units_btn, description_btn]
box75 = Box(children=row, layout=box_layout)
name_btn = Button(description='relative_maximum_volume', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'lightgreen'
self.float70 = FloatText(value='1.8', 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='max tolerated volume (relative to normal volume) before triggering apoptosis', 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='phagocytosis_rate', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'tan'
self.float71 = 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.float71, units_btn, description_btn]
box77 = Box(children=row, layout=box_layout)
name_btn = Button(description='phagocytosis_relative_target_cutoff_size', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'lightgreen'
self.float72 = FloatText(value='1.1', step='0.1', style=style, layout=widget_layout)
units_btn = Button(description='', disabled=True, layout=name_button_layout)
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.float72, units_btn, description_btn]
row = [name_btn, self.float70, units_btn, description_btn]
box78 = Box(children=row, layout=box_layout)
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.float73 = FloatText(value='1.0', step='0.1', style=style, layout=widget_layout)
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.float73, units_btn, description_btn]
row = [name_btn, self.float71, units_btn, description_btn]
box79 = Box(children=row, layout=box_layout)
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.float74 = FloatText(value='10.0', step='1', style=style, layout=widget_layout)
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.float74, units_btn, description_btn]
row = [name_btn, self.float72, units_btn, description_btn]
box80 = Box(children=row, layout=box_layout)
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.float75 = FloatText(value='0.4', step='0.1', style=style, layout=widget_layout)
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.float75, units_btn, description_btn]
row = [name_btn, self.float73, units_btn, description_btn]
box81 = Box(children=row, layout=box_layout)
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.float76 = FloatText(value='1', step='0.1', style=style, layout=widget_layout)
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.float76, units_btn, description_btn]
row = [name_btn, self.float74, units_btn, description_btn]
box82 = Box(children=row, layout=box_layout)
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.float77 = FloatText(value='0.0', step='0.01', style=style, layout=widget_layout)
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.float77, units_btn, description_btn]
row = [name_btn, self.float75, units_btn, description_btn]
box83 = Box(children=row, layout=box_layout)
box81 = 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,
......@@ -870,8 +850,6 @@ class CellTypesTab(object):
box79,
box80,
box81,
box82,
box83,
])
# ------------------------------------------
self.cell_def_vboxes.append(self.cell_def_vbox0)
......@@ -884,11 +862,11 @@ class CellTypesTab(object):
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.float78 = FloatText(value='0', step='0.01', style=style, layout=widget_layout)
self.float76 = FloatText(value='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 = 'lightgreen'
row = [name_btn, self.float78, units_btn, ]
box84 = Box(children=row, layout=box_layout)
row = [name_btn, self.float76, units_btn, ]
box82 = Box(children=row, layout=box_layout)
# -------------------------
div_row10 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout)
......@@ -901,7 +879,7 @@ class CellTypesTab(object):
# ================== <custom_data>, if present ==================
self.cell_def_vbox1 = VBox([
div_row9, death_model1,box84, div_row10, self.bool5,div_row11, ])
div_row9, death_model1,box82, div_row10, self.bool5,div_row11, ])
# ------------------------------------------
self.cell_def_vboxes.append(self.cell_def_vbox1)
......@@ -911,19 +889,19 @@ class CellTypesTab(object):
div_row12.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)
self.float77 = FloatText(value='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'
row = [name_btn, self.float79, units_btn, ]
box85 = Box(children=row, layout=box_layout)
row = [name_btn, self.float77, units_btn, ]
box83 = 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.float80 = FloatText(value='10', step='1', style=style, layout=widget_layout)
self.float78 = FloatText(value='10', step='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.float80, units_btn, ]
box86 = Box(children=row, layout=box_layout)
row = [name_btn, self.float78, units_btn, ]
box84 = Box(children=row, layout=box_layout)
# -------------------------
div_row13 = Button(description='phenotype:death', disabled=True, layout=divider_button_layout)
......@@ -932,11 +910,11 @@ class CellTypesTab(object):
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)
self.float79 = FloatText(value='5e-4', step='0.0001', style=style, layout=widget_layout)
units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout)
units_btn.style.button_color = 'tan'
row = [name_btn, self.float81, units_btn, ]
box87 = Box(children=row, layout=box_layout)
row = [name_btn, self.float79, units_btn, ]
box85 = Box(children=row, layout=box_layout)
# -------------------------
div_row14 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout)
......@@ -944,27 +922,27 @@ class CellTypesTab(object):
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)
self.float80 = 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]
box88 = Box(children=row, layout=box_layout)
row = [name_btn, self.float80, units_btn]
box86 = 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)
self.float81 = 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]
box89 = Box(children=row, layout=box_layout)
row = [name_btn, self.float81, units_btn]
box87 = 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)
self.float82 = 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]
box90 = Box(children=row, layout=box_layout)
row = [name_btn, self.float82, units_btn]
box88 = 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)
......@@ -977,13 +955,13 @@ class CellTypesTab(object):
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]
box91 = Box(children=row, layout=box_layout)
box89 = 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]
box92 = Box(children=row, layout=box_layout)
box90 = Box(children=row, layout=box_layout)
# -------------------------
div_row15 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout)
div_row15.style.button_color = 'orange'
......@@ -991,43 +969,43 @@ class CellTypesTab(object):
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]
box93 = Box(children=row, layout=box_layout)
box91 = 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)
self.float83 = 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]
box94 = Box(children=row, layout=box_layout)
row = [name_btn, self.float83, units_btn]
box92 = 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]
box95 = Box(children=row, layout=box_layout)
box93 = 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)
self.float84 = 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]
box96 = Box(children=row, layout=box_layout)
row = [name_btn, self.float84, units_btn]
box94 = 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]
box97 = Box(children=row, layout=box_layout)
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.float87 = FloatText(value='0.1', step='0.01', style=style, layout=widget_layout)
self.float85 = 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]
box98 = Box(children=row, layout=box_layout)
row = [name_btn, self.float85, units_btn]
box96 = Box(children=row, layout=box_layout)
# ================== <custom_data>, if present ==================
self.cell_def_vbox2 = VBox([
div_row12, box85, box86, div_row13, death_model1,box87, div_row14, box88,box89,box90,self.bool6,self.bool7,chemotaxis_btn,self.bool8,box91,box92,div_row15, box93,box94,box95,box96,box97,box98, ])
div_row12, box83, box84, div_row13, death_model1,box85, div_row14, box86,box87,box88,self.bool6,self.bool7,chemotaxis_btn,self.bool8,box89,box90,div_row15, box91,box92,box93,box94,box95,box96, ])
# ------------------------------------------
self.cell_def_vboxes.append(self.cell_def_vbox2)
......@@ -1039,11 +1017,11 @@ class CellTypesTab(object):
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)
self.float86 = FloatText(value='2.8e-4', step='1e-05', style=style, layout=widget_layout)
units_btn = Button(description='dimensionless', disabled=True, layout=name_button_layout)
units_btn.style.button_color = 'tan'
row = [name_btn, self.float88, units_btn, ]
box99 = Box(children=row, layout=box_layout)
row = [name_btn, self.float86, units_btn, ]
box97 = Box(children=row, layout=box_layout)
# -------------------------
div_row17 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout)
......@@ -1051,11 +1029,11 @@ class CellTypesTab(object):
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)
self.float87 = 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]
box100 = Box(children=row, layout=box_layout)
row = [name_btn, self.float87, units_btn]
box98 = 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)
......@@ -1068,31 +1046,31 @@ class CellTypesTab(object):
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]
box101 = Box(children=row, layout=box_layout)
box99 = 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]
box102 = Box(children=row, layout=box_layout)
box100 = Box(children=row, layout=box_layout)
# -------------------------
div_row18 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout)
div_row18.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)
self.float88 = 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'
row = [name_btn, self.float90, units_btn, ]
box103 = Box(children=row, layout=box_layout)
row = [name_btn, self.float88, units_btn, ]
box101 = Box(children=row, 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)
self.float89 = 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'
row = [name_btn, self.float91, units_btn, ]
box104 = Box(children=row, layout=box_layout)
row = [name_btn, self.float89, units_btn, ]
box102 = Box(children=row, layout=box_layout)
# -------------------------
div_row19 = Button(description='phenotype:secretion', disabled=True, layout=divider_button_layout)
......@@ -1101,14 +1079,14 @@ class CellTypesTab(object):
name_btn.style.button_color = 'tan'
self.text7 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long)
row = [name_btn, self.text7]
box105 = Box(children=row, layout=box_layout)
box103 = 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)
self.float90 = 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]
box106 = Box(children=row, layout=box_layout)
row = [name_btn, self.float90, units_btn]
box104 = Box(children=row, layout=box_layout)
# ================== <custom_data>, if present ==================
......@@ -1116,28 +1094,28 @@ class CellTypesTab(object):
div_row20.style.button_color = 'cyan'
name_btn = Button(description='cell_attachment_rate', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'tan'
self.float93 = FloatText(value='0.2', step='0.01', style=style, layout=widget_layout)
self.float91 = 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 = 'tan'
description_btn = Button(description='', disabled=True, layout=desc_button_layout)
description_btn.style.button_color = 'tan'
row = [name_btn, self.float93, units_btn, description_btn]
row = [name_btn, self.float91, units_btn, description_btn]
box107 = Box(children=row, layout=box_layout)
box105 = 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.float94 = FloatText(value='8.5', step='0.1', style=style, layout=widget_layout)
self.float92 = 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 = '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]
row = [name_btn, self.float92, units_btn, description_btn]
box108 = Box(children=row, layout=box_layout)
box106 = Box(children=row, layout=box_layout)
self.cell_def_vbox3 = VBox([
div_row16, death_model1,box99, div_row17, box100,self.bool9,self.bool10,chemotaxis_btn,self.bool11,box101,box102,div_row18, box103, box104, div_row19, box105,box106,div_row20, box107,
box108,
div_row16, death_model1,box97, div_row17, box98,self.bool9,self.bool10,chemotaxis_btn,self.bool11,box99,box100,div_row18, box101, box102, div_row19, box103,box104,div_row20, box105,
box106,
])
# ------------------------------------------
self.cell_def_vboxes.append(self.cell_def_vbox3)
......@@ -1150,11 +1128,11 @@ class CellTypesTab(object):
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.float95 = FloatText(value='2.1e-4', step='1e-05', style=style, layout=widget_layout)
self.float93 = FloatText(value='2.1e-4', step='1e-05', 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.float95, units_btn, ]
box109 = Box(children=row, layout=box_layout)
row = [name_btn, self.float93, units_btn, ]
box107 = Box(children=row, layout=box_layout)
# -------------------------
div_row22 = Button(description='phenotype:motility', disabled=True, layout=divider_button_layout)
......@@ -1162,19 +1140,19 @@ class CellTypesTab(object):
name_btn = Button(description='migration_bias', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'lightgreen'
self.float96 = FloatText(value='0.7', step='0.1', style=style, layout=widget_layout)
self.float94 = 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 = 'lightgreen'
row = [name_btn, self.float96, units_btn]
box110 = Box(children=row, layout=box_layout)
row = [name_btn, self.float94, units_btn]
box108 = 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.float97 = FloatText(value='5', step='0.1', style=style, layout=widget_layout)
self.float95 = 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.float97, units_btn]
box111 = Box(children=row, layout=box_layout)
row = [name_btn, self.float95, units_btn]
box109 = 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)
......@@ -1187,39 +1165,39 @@ class CellTypesTab(object):
name_btn.style.button_color = 'lightgreen'
self.chemotaxis_substrate5 = Text(value='debris', disabled=False, style=style, layout=widget_layout_long)
row = [name_btn, self.chemotaxis_substrate5]
box112 = Box(children=row, layout=box_layout)
box110 = 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_direction5 = Text(value='1', disabled=False, style=style, layout=widget_layout_long)
row = [name_btn, self.chemotaxis_direction5]
box113 = Box(children=row, layout=box_layout)
box111 = Box(children=row, layout=box_layout)
# -------------------------
div_row23 = Button(description='phenotype:volume', disabled=True, layout=divider_button_layout)
div_row23.style.button_color = 'orange'
name_btn = Button(description='total', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'lightgreen'
self.float98 = FloatText(value='4849', step='100', style=style, layout=widget_layout)
self.float96 = 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 = 'lightgreen'
row = [name_btn, self.float98, units_btn, ]
box114 = Box(children=row, layout=box_layout)
row = [name_btn, self.float96, units_btn, ]
box112 = Box(children=row, layout=box_layout)
name_btn = Button(description='nuclear', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'tan'
self.float99 = FloatText(value='485', step='10', style=style, layout=widget_layout)
self.float97 = 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 = 'tan'
row = [name_btn, self.float99, units_btn, ]
box115 = Box(children=row, layout=box_layout)
row = [name_btn, self.float97, units_btn, ]
box113 = 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.float100 = FloatText(value='0.01', step='0.001', style=style, layout=widget_layout)
self.float98 = 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 = 'lightgreen'
row = [name_btn, self.float100, units_btn, ]
box116 = Box(children=row, layout=box_layout)
row = [name_btn, self.float98, units_btn, ]
box114 = Box(children=row, layout=box_layout)
# ================== <custom_data>, if present ==================
......@@ -1228,61 +1206,61 @@ class CellTypesTab(object):
div_row24.style.button_color = 'cyan'
name_btn = Button(description='phagocytosis_rate', disabled=True, layout=name_button_layout)
name_btn.style.button_color = 'tan'
self.float101 = FloatText(value='0.167', step='0.01', style=style, layout=widget_layout)
self.float99 = 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.float101, units_btn, description_btn]
row = [name_btn, self.float99, units_btn, description_btn]
box117 = Box(children=row, layout=box_layout)
box115 = 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.float102 = FloatText(value='1.0', step='0.1', style=style, layout=widget_layout)
self.float100 = 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.float102, units_btn, description_btn]
row = [name_btn, self.float100, units_btn, description_btn]