Welcome to COBRA-k's documentation 😺

This documentation explains how to use the COBRA-k Python package, which is the reference implementation of COBRA-k (COnstraint-Based Reconstruction and Analysis with kinetics). To learn all about COBRA-k's main features, follow the numbered chapters on the left :-)

Info

At the start of many chapters, you may find a quickstart variant section, where a condensed down version of the chapter's code is presented.

Also note that, in this documentation's formulas, bold capital letters represent matrices (e.g. \(\mathbf{X}\)), bold small letters vectors (e.g. \(\mathbf{x}\)) and italic letters single numeric values (e.g. \(x\)).

For more about COBRA-k's features, code and license, visit its GitHub repository.

If you use COBRA-k in your academic work, please cite its publication:

[1] Bekiaris PS & Klamt S (2025). COBRA-k: a powerful framework bridging constraint-based and kinetic metabolic modeling. Submitted.