Guides¶
Curated, worked guides for common genome-scale metabolic modelling tasks. Step-by-step protocols are provided in both MATLAB and Python with code shown in MATLAB/Python tabs so you can follow along in either language.
Protocols¶
-
Homology-based reconstruction of a genome-scale model for the yeast Hansenula polymorpha (
hanpo-GEM), end to end — from template models to a growing, methylotrophic draft model.
Planned¶
These protocols are being added with MATLAB and Python variants:
- GEM extraction — extracting context-specific models.
- GEM comparison — comparing two models side by side.
Legacy tutorials¶
Five hands-on tutorials from the original RAVEN paper (Agren et al., 2013), updated to run with current RAVEN. MATLAB only.
| # | Tutorial | Topic |
|---|---|---|
| 1 | Import a GEM and run FBA | Load a model, set constraints, run FBA |
| 2 | Build a small model | Build from scratch in Excel |
| 3 | Knockouts, MOMA and omics | Gene deletions, MOMA, microarray data |
| 4 | Fix an erroneous model | Quality control and curation |
| 5 | Reconstruct from KEGG | De novo reconstruction from KEGG |