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:

Visualize

This subcommand creates .graphml files to be used by an external graph editor (yEd) for model visualization, including contact maps.

bionetgen visualize -i mymodel.bngl -o output_folder

You can see all the available options by running bionetgen visualize -h

optional arguments:
   -h, --help            show this help message and exit
-i INPUT, --input INPUT
                        Path to BNGL model to visualize
-o OUTPUT, --output OUTPUT
                        (optional) Output folder, defaults to current folder
-t TYPE, --type TYPE  (optional) Type of visualization requested. Valid options are: 'ruleviz_pattern','ruleviz_operation', 'contactmap', 'regulatory' and
                        'atom_rule'. Regulatory and atom rule graphs are the same thing, defaults to 'contactmap'.

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.

bionetgen info

Atomize

The CLI includes one more subcommand, atomize, which is detailed further in Atomizer.

Tutorial

For a brief tutorial showing how to use the CLI on a simple BNGL model, please see CLI Tutorial.