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>
......
This diff is collapsed.
This diff is collapsed.
......@@ -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'):
......
This diff is collapsed.
{
"cells": [
{
"cell_type": "code",
"execution_count": 1,
"metadata": {},
"outputs": [],
"source": [
"style = \"\"\"\n",
" <style>\n",
" .jupyter-widgets-output-area .output_scroll {\n",
" height: unset !important;\n",
" border-radius: unset !important;\n",
" -webkit-box-shadow: unset !important;\n",
" box-shadow: unset !important;\n",
" }\n",
" .jupyter-widgets-output-area {\n",
" height: auto !important;\n",
" width: 100%; !important;\n",
" }\n",
" </style>\n",
" \"\"\""
]
},
{
"cell_type": "code",
"execution_count": 2,
"metadata": {
"extensions": {
"jupyter_dashboards": {
"version": 1,
"views": {
"grid_default": {
"hidden": true
},
"report_default": {
......@@ -28,5 +53,11 @@
" box-shadow: unset !important;\n",
" }\n",
" .jupyter-widgets-output-area {\n",
" height: auto !important;\n",
" width: 100%; !important;\n",
" }\n",
" </style>\n",
" "
],
"text/plain": [
"<IPython.core.display.HTML object>"
......
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
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
This diff is collapsed.
Markdown is supported
0% or .
You are about to add 0 people to the discussion. Proceed with caution.
Finish editing this message first!
Please register or to comment