Commit 2aa35629 authored by Randy Heiland's avatar Randy Heiland
Browse files

cleanup

parent e19aca7a
BSD 3-Clause License
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# pc4covid19 - COVID19 (SARS-CoV-2) tissue simulator nanoHUB app
**Version:** 3.0
**Release date:** 3 July 2020
## Overview
This repository contains code and data for the nanoHUB app https://nanohub.org/tools/pc4covid19.
Here, we primarily report on changes to the app's GUI.
It is based on the model at https://github.com/pc4covid19/COVID19. Refer to that repository
for a summary of changes to the model.
### Caveats and disclaimers:
**This model is under active development using rapid prototyping:**
* It has not been peer reviewed.
* It is intended to drive basic scientific research and public education at this stage.
* **It cannot be used for public policy decisions.**
* **It cannot be used for individual medical decisions.**
**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:
### 3.0:
The major change to the GUI in this release is the addition of a 'Cell Types' tab.
This allows editing parameters associated with `<cell_definitions>` in the configuration file.
This version also includes a `<style>` block in the Jupyter notebook that fixed an unwanted scrollbar in the lengthy `About` tab.
### 2.0:
The major change to the GUI in this release is the addition of an 'Animate' tab.
This allows animation of cells (not substrates) in the tab and the generation of a .mp4
video that can be downloaded. The animation uses the cells' SVG files.
### 1.0:
Provides a "standard" PhysiCell-based Jupyter notebook GUI consisting of 5 tabs:
* About: a description of the model and the app
* Config Basics: input parameters common to all models (e.g., domain grid, simulation time, choice/frequency of outputs)
* Microenvironment: microenvironment parameters that are model-specific
* User Params: user parameters that are model-specific
* Out: Plots: output display of cells and substrates
diff -r src/BioFVM/ ~/dev/COVID19-dev/PhysiCell/BioFVM/
diff -r src/core/ ~/dev/COVID19-dev/PhysiCell/core/
diff -r src/custom_modules/ ~/dev/COVID19-dev/PhysiCell/custom_modules/
diff data/PhysiCell_settings.xml ~/dev/COVID19-dev/PhysiCell/config/PhysiCell_settings.xml
%% Cell type:code id: tags:
``` python
%matplotlib inline
#from IPython.core.display import display, HTML
#display(HTML("<style>.container { width:100% !important; }</style>"))
```
%% Cell type:code id: tags:
``` python
import sys, os
sys.path.insert(0, os.path.abspath('bin'))
import pc4covid19
```
%%%% Output: display_data
%% Cell type:code id: tags:
``` python
pc4covid19.gui
```
%%%% Output: display_data
%% Cell type:code id: tags:
``` python
#from debug import debug_view
#debug_view
```
%% Cell type:code id: tags:
``` python
```
%% 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: display_data
%% Cell type:code id: tags:
``` python
import sys, os
sys.path.insert(0, os.path.abspath('bin'))
import pc4covid19
```
%%%% Output: display_data
%% Cell type:code id: tags:
``` python
pc4covid19.gui
```
%%%% Output: display_data
%% Cell type:code id: tags:
``` python
#from debug import debug_view
#debug_view
```
%% Cell type:code id: tags:
``` python
```
%% 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;
}
</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: display_data
%% Cell type:code id: tags:
``` python
import sys, os
sys.path.insert(0, os.path.abspath('bin'))
import pc4covid19
```
%% Cell type:code id: tags:
``` python
pc4covid19.gui
```
%%%% Output: display_data
%% Cell type:code id: tags:
``` python
#from debug import debug_view
#debug_view
```
%% Cell type:code id: tags:
``` python
```
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