rheiland / binder-test

Jupyter Notebook GUI for a PhysiCell project

This project requires a Python distribution with modules not found in the standard library. In particular, it needs matplotlib (and all its dependencies), scipy.io, and Jupyter (notebooks). You have at least a couple of different options:

1. Perhaps the easiest way to get all of this is to download and install the Anaconda Python 3.x distribution: https://www.anaconda.com/download/ however, that distribution (which includes a LOT of additional modules), is ~500-600MB.

2. If you want to downlod a much smaller bundle, but in multiple steps, you could try to:

• download the Miniconda Python 3.x installer (preferably 64-bit): (~30 MB) https://conda.io/miniconda.html

then install the additional, required modules:

conda install matplotlib
conda install scipy
conda install jupyter

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After you have the desired Python modules:

• Copy your project's configuration file (.xml) to this directory, calling it "myconfig.xml"
• Copy your project's executable to this directory, e.g., heterogeneity, in the example below.
• Generate the Python module of widgets for your user params (a "tab" in the Notebook GUI). From a Terminal/Command Prompt window, run:

python gen_user_tab.py myconfig.xml

Then run the notebook:

jupyter notebook PhysiCell.ipynb

Make changes to the configuration parameters via the Jupyter notebook GUI, press the 'Write' button, then run your simulation from a shell window, e.g.:

heterogeneity myconfig.xml

If you don't have your current working directory in your PATH, you will need to be more explicit, e.g.:

./heterogeneity myconfig.xml     # on Unix
.\heterogeneity myconfig.xml     # on Windows

Click the binder badge to play with the notebook from your browser without installing anything.