Tools for working with RDF descriptions of bondgraphs

Constructing branching (vascular) bondgraph models from templates

Two separate sets of RDF are used:

1. Template descriptions, such as vascular-segment-template.ttl.
2. A model definition specifies how templates are connected and parameterised to form a model.
3. Examples of using vascular-segment-template.ttl are:
   1. single-segment.ttl defines a single straight segment.
   2. stomach-spleen.ttl defines a branching network representing stomach/spleen vasculature.

More details are in the notes.

Installation pre-requisites

• Python 3.12
• Poetry package manager
• Poetry's Monoranger plugin.

Installation

$ git clone https://github.com/CellDL/bondgraph-tools.git
$ cd bondgraph-tools
$ poetry install

Running

Activate the Python virtual environment:

$ source .venv/bin/activate

Command line help:

$ python rdf2cellml.py --help
usage: rdf2cellml.py [-h] [--version] [--celldl CELLDL_FILE] TEMPLATE_FILE MODEL_FILE CELLML_FILE
Generate CellML for a bondgraph model specified in RDF
positional arguments:
TEMPLATE_FILE A template file defining bondgraph components in RDF
MODEL_FILE The RDF definition of a model
CELLML_FILE The name for the resulting CellML file
options:
-h, --help show this help message and exit
--version show program's version number and exit
--celldl CELLDL_FILE The name for the CellDL (SVG) output file. Optional