Tutorial

BioSimulators-BioNetGen is available as a command-line program and as a command-line program encapsulated into a Docker image.

Creating COMBINE/OMEX archives and encoding simulation experiments into SED-ML

Information about how to create COMBINE/OMEX archives which can be executed by BioSimulators-BioNetGen is available at BioSimulators.

A list of the algorithms and algorithm parameters supported by BioNetGen is available at BioSimulators.

Targets for encoding changes to model parameters into SED-ML

The following targets should be used to encode changes to model parameters into SED-ML.

  • Compartment sizes: targets should follow the pattern compartments.<compartment_id>.size. E.g.:

    <sedml:changeAttribute target="compartments.Compartment_C.size" newValue="1e-6" />
    
  • Function expressions: targets should follow the pattern functions.<function_id>.expression. E.g.:

    <sedml:changeAttribute target="functions.gfunc.expression" newValue="0.5" />
    
  • Function arguments and expressions: targets should follow the pattern functions.<function_id>(<args>).expression. E.g.:

    <sedml:changeAttribute target="functions.gfunc().expression" newValue="0.5" />
    
  • Initial species counts: targets should follow the pattern species.<species_id>.initialCount. E.g.:

    <sedml:changeAttribute target="species.GeneA_00().initialCount" newValue="10" />
    
  • Parameter values: targets should follow the pattern parameters.<parameter_id>.value. E.g.:

    <sedml:changeAttribute target="parameters.k_1.value" newValue="2.0" />
    

Targets for encoding the desired observables into SED-ML

The following patterns should be used to encode the desired observables of a simulation into SED-ML.

  • Species: targets for species counts and concentrations should follow the pattern species.<species_id>.count. E.g.:

    <sedml:dataGenerator id="data_generator_species_A">
      <listOfVariables>
        <sedml:Variable id="variable_species_A" target="species.A().count" taskReference="taskId" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci>variable_species_A</ci>
      </math>
    </sedml:dataGenerator>
    
  • Molecules: targets for molecule counts and concentrations should follow the pattern molecules.<molecule_pattern>.count. E.g.:

    <sedml:dataGenerator id="data_generator_molecule_B">
      <listOfVariables>
        <sedml:Variable id="variable_molecule_B" target="molecules.B().count" taskReference="taskId" />
      </listOfVariables>
      <math xmlns="http://www.w3.org/1998/Math/MathML">
        <ci>variable_molecule_B</ci>
      </math>
    </sedml:dataGenerator>
    

Command-line program

The command-line program can be used to execute COMBINE/OMEX archives that describe simulations as illustrated below.

usage: bionetgen [-h] [-d] [-q] -i ARCHIVE [-o OUT_DIR] [-v]

BioSimulators-compliant command-line interface to the BioNetGen <https://bionetgen.org> simulation program.

optional arguments:
  -h, --help            show this help message and exit
  -d, --debug           full application debug mode
  -q, --quiet           suppress all console output
  -i ARCHIVE, --archive ARCHIVE
                        Path to OMEX file which contains one or more SED-ML-
                        encoded simulation experiments
  -o OUT_DIR, --out-dir OUT_DIR
                        Directory to save outputs
  -v, --version         show program's version number and exit

For example, the following command could be used to execute the simulations described in ./modeling-study.omex and save their results to ./:

bionetgen -i ./modeling-study.omex -o ./

Docker image with a command-line entrypoint

The entrypoint to the Docker image supports the same command-line interface described above.

For example, the following command could be used to use the Docker image to execute the same simulations described in ./modeling-study.omex and save their results to ./:

docker run \
    --tty \
    --rm \
    --mount type=bind,source="$(pwd),target=/tmp/working-dir \
    ghcr.io/biosimulators/bionetgen:latest \
        -i /tmp/working-dir/modeling-study.omex \
        -o /tmp/working-dir