BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways
Vladislav A. Kachnov, Maryam A. Esembaeva, Ekaterina V. Melikhova, Mikhail A. Kulyashov · 2026
Read BioEMMA: Automated Generation of Model-Specific Escher-Compatible Maps from KEGG Pathways by Vladislav A. Kachnov, Maryam A. Esembaeva, Ekaterina V. Melikhova, Mikhail A. Kulyashov (2026) in the Tower of Babel, a free online library of public-domain works preserved in clean, searchable text. No sign-up. The full text is served as a plain-text file at a predictable URL, where text is present: https://antarctic-labs.com/tower-of-babel/pmc-13564630.txt.
Description
Vladislav A Kachnov and co-authors automate the drawing of readable maps for genome-scale metabolism models. Such models list thousands of reactions, but without a shared map layout their pathways are hard to read or compare. Their tool, BioEMMA, borrows coordinates from curated KEGG pathway maps and rebuilds them in Escher's format, filtered to just the reactions a given model actually has.
Tested first on a core Escherichia coli model with simulated fluxes painted onto glycolysis, the tool then compared models rebuilt by three different pipelines. It was also run across ninety bacterial and yeast models from a standard library. Coverage and flux patterns differed by pathway and builder, exactly the contrasts the maps exist to expose. The authors offer BioEMMA inside a reproducible workflow.
Catalog record
| CREATOR | Vladislav A. Kachnov, Maryam A. Esembaeva, Ekaterina V. Melikhova, Mikhail A. Kulyashov |
|---|---|
| YEAR | 2026 |
| COLLECTION | PAPERS |
| FORMAT | TXT |
| FILE SIZE | 68 KB |
| VERSION | 1.0 |
| LICENSE | CC BY 4.0 |
| RIGHTS | CC BY |
| SOURCE | Europe PMC |