Tutorial

BioSimulators-XPP 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-XPP is available at BioSimulators.

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

Models (XPP)

BioSimulators-XPP can execute models encoded in XPP format (urn:sedml:language:xpp).

Simulation experiments (SED-ML, KISAO)

BioSimulators-XPP can execute simulation experiments encoded in SED-ML, using KiSAO to indicate specific algorithms and their parameters. Information about the algorithms (KiSAO terms), algorithm parameters (KiSAO terms), and outputs (names for variables) supported by BioSimulators-XPP is available from the BioSimulators registry.

Models (sedml.Model)

Models should be specified using language URN urn:sedml:language:xpp. Model sources can be specified in two ways:

  • Path to .ode files.

  • Directories which contain .ode and optionally set (.set), parameter (.par), and/or initial conditions (.ic) files. .set, .par, and .ic files can have any filename that ends in these extensions. Directories should contain at most one of each of these three types of files. If supplied, the content of``.set`` files first overrides .ode files and then .par and .ic files can further override definitions of models.

<model id="model" language="urn:sedml:language:xpp" source="model.ode" />

Targets for model changes (sedml.AttributeChange)

Targets for changes to model parameters should be encoded using the name of the parameter as target="{ parameter name }" such as target="k1". The names are parameters are not case sensitive.:

<attributeChange target="k1" newValue="0.1" />

Targets for changes to initial conditions should be encoded using the name of the variable as target="{ variable name }" such as target="X". The names are variables are not case sensitive.:

<attributeChange target="X" newValue="10.0" />

Simulations (sedml.UniformTimeCourse, sedml.Algorithm)

Simulations should be encoded using the UniformTimeCourse class with simulation algorithms such as KISAO_0000019 (CVODE) and algorithm parameters such as KISAO_0000209 (relative tolerance). Information about the algorithm and algorithm parameter KiSAO terms recognized by BioSimulators-XPP is available from the BioSimulators registry.:

<uniformTimeCourse id="simulation">
  <algorithm kisaoID="KISAO:0000019">
     <algorithmParameter kisaoID="KISAO:0000209" newValue="1e-9" />
  </algorithm>
</uniformTimeCourse>

Targets for observables (sedml.Variable of sedml.DataGenerator)

Targets for XPP variables should be encoded using the name of the variable as target="{ variable name }" such as target="X". The names are variables are not case sensitive.:

<dataGenerator id="data_generator_X">
  <math xmlns="http://www.w3.org/1998/Math/MathML">
    <ci> variable_X </ci>
  </math>
  <listOfVariables>
    <variable id="variable_X" target="X" taskReference="task"/>
  </listOfVariables>
</dataGenerator>

Example COMBINE/OMEX archives

Examples of COMBINE/OMEX archives for simulations which BioSimulators-XPP can execute are available in the BioSimulators test suite.

Command-line program

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

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

BioSimulators-compliant command-line interface to the XPP <http://www.math.pitt.edu/~bard/xpp/xpp.html> 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 ./:

biosimulators-xpp -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/xpp:latest \
        -i /tmp/working-dir/modeling-study.omex \
        -o /tmp/working-dir