Conceptual and API reference for raven-toolbox.
- RAVEN ↔ raven-toolbox migration map — the function-by-function map from MATLAB RAVEN to raven-toolbox (and cobrapy where appropriate). Start here if you're porting RAVEN code.
- YAML model format — the shared YAML schema produced and consumed by cobrapy, raven-toolbox, and RAVEN MATLAB, with a fully-annotated example and the field-order / quoting rules.
- MATLAB RAVEN back-port proposals — improvements raven-toolbox makes that are candidates to back-port into the MATLAB toolbox.
- Improvements over RAVEN — the full catalogue of correctness /
ergonomics improvements (the
IMPROVEMENTS.mdmaster list). - API reference — every public function and class, generated from the docstrings.
- Gap-filling algorithms — literature review — survey of published gap-filling methods with formulation, trade-offs, and implementation recommendations.
- COBRA vs RAVEN comparison — feature-by-feature comparison of the COBRA Toolbox and RAVEN Toolbox, identifying gaps and overlap.
- Markov-chain flux sampling — CHRR and ACHR — algorithm description, implementation notes, and guidance on when to use each method.
- Evidence-aware transport scoring — design & plan — a cross-repo (RAVEN + raven-toolbox) plan to replace the blanket transport penalty in localisation with transporter-evidence-weighted costs; carrier-general, organism-agnostic, local-binary-based.
- Sound reaction-level multi-localisation — design — why naive
multi-localisation admits dead placements, and the ε-flux activity-coupling formulation
assign_compartmentsuses to forbid them (solver-independent).
:hidden:
migration
yaml_format
matlab_raven_backports
improvements
api/index
gap_filling_algorithms
cobra_raven_comparison
flux_sampling_algorithms
transport_evidence_scoring
multi_localization_design