CLI Tutorial

This tutorial shows how to use PyBioNetGen’s command line interface to run and plot a simple BNGL model, as well as how to create a simple Jupyter notebook containing the model, using the simple “SIR.bngl” model as an example.

Getting Started

Make sure you have PyBioNetGen properly installed by running

bionetgen -h

If this command doesn’t print out help information, install PyBioNetGen with

pip install bionetgen

Running a Model

To first run your model in a new or existing folder called “SIR_folder”, use the run subcommand:

bionetgen run -i SIR.bngl -o SIR_folder

This will run the model and save the results under the specified folder, allowing for further analysis.

Plotting a Model

To simply plot the gdat or cdat file, use the plot subcommand with the appropriate file:

bionetgen plot -i SIR.gdat

The resulting gdat plot should look like this:

However, there are many optional arguments, such as including a legend or changing axes. Use bionetgen plot -h to see them. For example, if we wanted to look at a smaller timeframe, change some labels, and include a legend, we would run:

bionetgen plot -i SIR.gdat --legend --xmax 10 --ylabel "individuals" --title "SIR Populations"

The updated plot should look like this:

Creating a Notebook

Finally, use the notebook subcommand to create a Jupyter notebook:

bionetgen notebook -i SIR.bngl -o SIR_notebook.ipynb

This subcommand currently has limited functionality, and will only create a simple notebook that can run and plot the model.