SPARCED Hands-On Primer Tutorial¶

Welcome to the SPARCED Hands-On Primer Tutorial! This guide walks you through how to run the Python files in the SPARCED package for tasks like model compilation, simulations, benchmarking, and visualizations.

Prerequisites¶

Before running the Python files, ensure you have the following installed:

  1. Python 3.10+

  2. Required dependencies from requirements.txt: Run:

    chmod +x requirements.txt
./requirements.txt

  3. SPARCED source code properly cloned or installed.

Running Python Scripts¶

The SPARCED package provides various utilities for simulations, benchmarks, and data visualization. Below are the key Python files and their purposes.

Model Compilation¶

To compile a model using Antimony or SBML, use the following script:

python src/compilation/create_model.py --input <path/to/model/file> --output <path/to/output>

Replace <path/to/model/file> with the location of your Antimony or SBML model and <path/to/output> with the desired output path.

Simulation Execution¶

Run a simulation using pre-defined models and conditions:

python src/simulation/run_model.py --model SPARCED_standard --condition <condition_file>

  • –model: Specify the model name (e.g., SPARCED_standard).

  • –condition: Path to the condition file for the simulation.

For example:

python src/simulation/run_model.py --model SPARCED_standard --condition data/simulation/standard_GeneReg.txt

Benchmark Generation¶

To generate a benchmark, use:

python src/benchmarking/creation/new-benchmark-generator.py --output benchmarks/new_benchmark.yml

This will create a new benchmark YAML file in the specified location.

Benchmark Validation¶

To validate a model against a benchmark:

python src/benchmarking/simulation/model-benchmark-validation.py --benchmark benchmarks/new_benchmark.yml

Visualization¶

Visualize simulation results using:

python src/benchmarking/visualization/visualization.py --input <path/to/results> --output <path/to/visualization>

This script processes the results and generates graphical outputs.

Key Examples¶

Here are some hands-on examples to get you started:

  1. Running a Simple Model Simulation: .. code-block:: bash

    python src/simulation/run_model.py –model SPARCED_standard –condition data/simulation/standard_GeneReg.txt

  2. Validating a Model Against Benchmarks: .. code-block:: bash

    python src/simulation/model-benchmark-validation.py –benchmark benchmarks/TRAIl_percent-death.yml

  3. Generating a Custom Visualization: .. code-block:: bash

    python src/visualization/visualization.py –input results/New-Simulation/Control –output figures/Control_Visualization.png

Additional Resources¶

  • For more details, refer to the SPARCED Documentation.

  • Check out the Jupyter notebooks in the examples/notebooks directory for interactive tutorials.

Questions or Issues?¶

If you encounter any issues, feel free to open an issue on the GitHub repository or contact the SPARCED support team.