pipeGEM

pipeGEM provides Python and CLI workflows for working with genome-scale metabolic models. It wraps common model operations, expression-data integration, medium handling, metabolic tasks, flux analysis, and model comparison around COBRA models.

Where to start

• New installation: Installation
• First model workflow: Quickstart
• Notebook walkthroughs: Tutorials
• Task-oriented reference: User guide
• Python objects and functions: API reference

Common workflows

1. Load a COBRA model with pipeGEM.load_model.
2. Wrap it in pipeGEM.Model for annotation, data, task, and analysis helpers.
3. Add gene expression data with pipeGEM.data.GeneData.
4. Add medium constraints with pipeGEM.data.MediumData or the built-in medium catalog.
5. Run thresholding, model extraction, task testing, or flux analysis.
6. Compare multiple models with pipeGEM.Group.

What changed from the old docs?

The Sphinx documentation has moved to MkDocs Material. The old topics are still present, but the navigation is organized by workflow:

• quickstart.html is now Getting Started > Quickstart.
• tutorial/index.html is now Tutorials.
• api/index.html is now API Reference.
• Sphinx internals such as genindex, modindex, and _sources are no longer generated.

The CLI examples now use the current subcommand form, such as pipeGEM template, pipeGEM process, and pipeGEM integrate. The old -n <pipeline> form remains available for compatibility but is deprecated.

Build these docs locally

The documentation build is driven by the doc optional dependency group in pyproject.toml:

uv run --extra doc mkdocs build --strict -d ./docs

Read the Docs uses the same command and publishes the generated HTML from its configured output directory.