Command Line Interface
The command line tool comes with several subcommands. For each command, you can see the help text with the command
bionetgen subcommand -h
Run
This subcommand simply runs a model:
bionetgen run -i mymodel.bngl -o output_folder
This will run mymodel.bngl
under the folder output_folder
.
If no output folder is specified, then the temporary folder used while running the subcommand will be deleted upon completion.
Plot
This subcommand allows you to make a simple plot from a gdat/cdat or scan file:
bionetgen plot -i mymodel.gdat -o gdat_plot.png
You can see all the available options by running bionetgen plot -h
optional arguments:
-h, --help show this help message and exit
-i INPUT, --input INPUT
Path to .gdat/.cdat file to use plot
-o OUTPUT, --output OUTPUT
Optional path for the plot (default:
"$model_name.png")
--legend To plot the legend or not (default: False)
--xmin XMIN x-axis minimum (default: determined from data)
--xmax XMAX x-axis maximum (default: determined from data)
--ymin YMIN y-axis minimum (default: determined from data)
--ymax YMAX y-axis maximum (default: determined from data)
--xlabel XLABEL x-axis label (default: time)
--ylabel YLABEL y-axis label (default: concentration)
--title TITLE title of plot (default: determined from input file)
Resulting plots should look similar to this:

Notebook
This subcommand is in its early stages of development. The subcommand is used to generate a simple Jupyter notebook. You can also give your model as an argument and the resulting notebook will be ready to load in your model using PyBioNetGen library.
bionetgen notebook -i mymodel.bngl -o mynotebook.ipynb
Info
This subcommand simply prints out information about software versions and installation paths.
Tutorial
For a brief tutorial showing how to use the CLI on a simple BNGL model, please see CLI Tutorial.