gemiz
An alpha FASTA-to-SBML toolkit for bacterial genome-scale metabolic reconstruction, combining pyrodigal gene calling, MMseqs2 reaction scoring, COBRApy/HiGHS model assembly, and inspectable evidence and quality-control artifacts.
What I did
I built the reconstruction pipeline and the benchmark setup.
Why I built it
Turning a bacterial genome into a usable metabolic model requires more than annotation: every reaction needs traceable evidence, the assembled network needs validation, and the result has to be reproducible.
How it works
gemiz calls genes with pyrodigal, scores reaction evidence with MMseqs2, assembles and checks the network with COBRApy and HiGHS, and exports SBML together with inspectable evidence and QC artifacts.
What came out of it
- Produces a complete FASTA-to-SBML reconstruction workflow for bacterial genomes.
- Keeps reaction evidence and quality checks alongside the final model.
- Supports reproducible comparisons with CarveMe and gold-standard models.
Main pieces
- pyrodigal for bacterial gene calling.
- MMseqs2 for sequence-based reaction scoring.
- COBRApy, HiGHS, and SBML for model assembly, solving, and export.
What I would improve
The public alpha currently focuses on bacterial genomes. Eukaryotic support and experimental embedding-based scoring remain outside the supported public workflow.