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:

_images/SIR.png

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.