PhysiCelldFBA/dfba_sbml_models: PhysiCelldFBA Models Paper Release

This is the first public release of dfba_sbml_models, accompanying the PhysiCelldFBA manuscript. The repository provides the curated genome-scale metabolic models and preprocessing workflow used in the simulation case studies presented in the paper. Included models Escherichia coli core metabolic model iML1515 (Escherichia coli) iCB925 (Clostridium beijerinckii) iMG746 (Methanosarcina barkeri Fusaro) MCF7 genome-scale metabolic model from Zielinski et al. (2017) Repository contents Scripts to retrieve publicly available metabolic models. Model-specific preprocessing notebooks. Automated preprocessing pipeline (prepare_models.py). Curated SBML models used in the PhysiCelldFBA manuscript. Documentation describing the complete curation workflow. The original metabolic reconstructions remain the work of their respective authors. This repository provides the curated versions and preprocessing workflow required to reproduce the PhysiCelldFBA simulation examples. If you use this repository, please cite: the original publications describing the metabolic models; the PhysiCelldFBA publication; the Zenodo archive associated with this release.