Commit 3b61c022 authored by Randy Heiland's avatar Randy Heiland
Browse files

v3

parent afb44c5e
......@@ -11,9 +11,9 @@
</software>
<citation />
<current_time units="min">0.000000</current_time>
<current_runtime units="sec">0.041417</current_runtime>
<created>2020-04-10T10:09:51Z</created>
<last_modified>2020-04-10T10:09:51Z</last_modified>
<current_runtime units="sec">0.074109</current_runtime>
<created>2020-06-29T13:38:32Z</created>
<last_modified>2020-06-29T13:38:32Z</last_modified>
</metadata>
<microenvironment>
<domain name="microenvironment">
......@@ -27,20 +27,48 @@
</voxels>
</mesh>
<variables>
<variable name="virion" units="virion/um^3" ID="0">
<variable name="virion" units="virion/micron^3" ID="0">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">90.000000</diffusion_coefficient>
<diffusion_coefficient units="micron^2/min">2.500000</diffusion_coefficient>
<decay_rate units="1/min">0.000000</decay_rate>
</physical_parameter_set>
</variable>
<variable name="assembled virion" units="virion/um^3" ID="1">
<variable name="assembled virion" units="virion/micron^3" ID="1">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">90.000000</diffusion_coefficient>
<diffusion_coefficient units="micron^2/min">2.500000</diffusion_coefficient>
<decay_rate units="1/min">0.000000</decay_rate>
</physical_parameter_set>
</variable>
<variable name="interferon 1" units="mol/micron^3" ID="2">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
<decay_rate units="1/min">0.010200</decay_rate>
</physical_parameter_set>
</variable>
<variable name="pro-inflammatory cytokine" units="mol/micron^3" ID="3">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
<decay_rate units="1/min">0.010200</decay_rate>
</physical_parameter_set>
</variable>
<variable name="chemokine" units="mol/micron^3" ID="4">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
<decay_rate units="1/min">0.010200</decay_rate>
</physical_parameter_set>
</variable>
<variable name="debris" units="mol/micron^3" ID="5">
<physical_parameter_set>
<conditions />
<diffusion_coefficient units="micron^2/min">555.560000</diffusion_coefficient>
<decay_rate units="1/min">0.010200</decay_rate>
</physical_parameter_set>
</variable>
</variables>
<data type="matlab">
<filename>initial_microenvironment0.mat</filename>
......@@ -75,27 +103,44 @@
<label index="22" size="3">motility_bias_direction</label>
<label index="25" size="1">persistence_time</label>
<label index="26" size="1">motility_reserved</label>
<label index="27" size="1">unbound external ACE2</label>
<label index="28" size="1">bound external ACE2</label>
<label index="29" size="1">unbound internal ACE2</label>
<label index="30" size="1">bound internal ACE2</label>
<label index="31" size="1">ACE2 binding rate</label>
<label index="32" size="1">ACE2 endocytosis rate</label>
<label index="33" size="1">ACE2 cargo release rate</label>
<label index="34" size="1">ACE2 recycling rate</label>
<label index="35" size="1">virion</label>
<label index="36" size="1">uncoated virion</label>
<label index="37" size="1">viral RNA</label>
<label index="38" size="1">viral protein</label>
<label index="39" size="1">assembled virion</label>
<label index="40" size="1">virion uncoating rate</label>
<label index="41" size="1">uncoated to RNA rate</label>
<label index="42" size="1">protein synthesis rate</label>
<label index="43" size="1">virion assembly rate</label>
<label index="44" size="1">virion export rate</label>
<label index="45" size="1">max infected apoptosis rate</label>
<label index="46" size="1">max apoptosis half max</label>
<label index="47" size="1">apoptosis hill power</label>
<label index="27" size="1">virion</label>
<label index="28" size="1">uncoated_virion</label>
<label index="29" size="1">viral_RNA</label>
<label index="30" size="1">viral_protein</label>
<label index="31" size="1">assembled_virion</label>
<label index="32" size="1">virion_uncoating_rate</label>
<label index="33" size="1">uncoated_to_RNA_rate</label>
<label index="34" size="1">protein_synthesis_rate</label>
<label index="35" size="1">virion_assembly_rate</label>
<label index="36" size="1">virion_export_rate</label>
<label index="37" size="1">unbound_external_ACE2</label>
<label index="38" size="1">bound_external_ACE2</label>
<label index="39" size="1">unbound_internal_ACE2</label>
<label index="40" size="1">bound_internal_ACE2</label>
<label index="41" size="1">ACE2_binding_rate</label>
<label index="42" size="1">ACE2_endocytosis_rate</label>
<label index="43" size="1">ACE2_cargo_release_rate</label>
<label index="44" size="1">ACE2_recycling_rate</label>
<label index="45" size="1">max_infected_apoptosis_rate</label>
<label index="46" size="1">max_apoptosis_half_max</label>
<label index="47" size="1">apoptosis_hill_power</label>
<label index="48" size="1">virus_fraction_released_at_death</label>
<label index="49" size="1">infected_cell_chemokine_secretion_rate</label>
<label index="50" size="1">debris_secretion_rate</label>
<label index="51" size="1">infected_cell_chemokine_secretion_activated</label>
<label index="52" size="1">TCell_contact_time</label>
<label index="53" size="1">cell_attachment_rate</label>
<label index="54" size="1">cell_attachment_lifetime</label>
<label index="55" size="1">TCell_contact_death_threshold</label>
<label index="56" size="1">max_attachment_distance</label>
<label index="57" size="1">elastic_attachment_coefficient</label>
<label index="58" size="1">relative_maximum_volume</label>
<label index="59" size="1">phagocytosis_rate</label>
<label index="60" size="1">sensitivity_to_debris_chemotaxis</label>
<label index="61" size="1">sensitivity_to_chemokine_chemotaxis</label>
<label index="62" size="1">activated_speed</label>
<label index="63" size="1">activated_cytokine_secretion_rate</label>
<label index="64" size="1">activated_immune_cell</label>
</labels>
<filename>initial_cells_physicell.mat</filename>
</simplified_data>
......
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......@@ -280,7 +280,7 @@ for child in uep: # uep = "unique entry point" for <user_parameters> (from abo
else:
describe_str = ""
desc_row_name = "desc_button" + str(param_count)
desc_buttons_str += indent + desc_row_name + " = " + "Button(description='" + describe_str + "', disabled=True, layout=desc_button_layout) \n"
desc_buttons_str += indent + desc_row_name + " = " + "Button(description='" + describe_str + "' , tooltip='" + describe_str + "', disabled=True, layout=desc_button_layout) \n"
# print("--- debug: " + desc_row_name + " --> " + describe_str) #rwh debug
if (param_count % 2):
......@@ -593,6 +593,7 @@ if uep:
# 1) Variable name + [units]
menv_var_name_button = "menv_var" + str(menv_var_count)
menv_var_name = var.attrib['name'].replace(" ","_") # e.g., "director signal" --> "director_signal"
menv_var_name = menv_var_name.replace("-","_") # e.g., "pro-inflammatory_cytokine" --> "pro_inflammatory_cytokine"
print('menv_var_name=',menv_var_name)
units_str = ''
if ('units' in var.attrib) and (var.attrib['units'] != 'dimensionless'):
......
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%% Cell type:code id: tags:
``` python
style = """
<style>
.jupyter-widgets-output-area .output_scroll {
height: unset !important;
border-radius: unset !important;
-webkit-box-shadow: unset !important;
box-shadow: unset !important;
}
.jupyter-widgets-output-area {
height: auto !important;
width: 100%; !important;
}
</style>
"""
```
%% Cell type:code id: tags:
``` python
%matplotlib inline
from IPython.core.display import display, HTML
# display(HTML("<style>.container { width:100%; !important; }</style>"))
display(HTML(style))
```
%% Output
%% Cell type:code id: tags:
``` python
import sys, os
sys.path.insert(0, os.path.abspath('bin'))
import pc4covid19
```
%% Output
%% Cell type:code id: tags:
``` python
pc4covid19.gui
```
%% Output
%% Cell type:code id: tags:
``` python
#from debug import debug_view
#debug_view
```
%% Cell type:code id: tags:
``` python
```
......
Using PhysiCell version 1.7.0-dev
Using PhysiCell version 1.7.1
Please cite DOI: 10.1371/journal.pcbi.1005991
Project website: http://PhysiCell.MathCancer.org
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