Table 6.
List of software for genome-scale metabolic reconstruction and constraint-based modeling.
| Software (implementation) | Application | References |
|---|---|---|
| COBRA (Matlab) | Genome-scale reconstruction and constraint-based modeling | Heirendt et al., 2019 |
| RAVEN (Matlab) | Genome-scale reconstruction and constraint-based modeling | Wang et al., 2018 |
| CarveME (Python) | Genome-scale reconstruction | Machado et al., 2018 |
| gapseq (R) | Genome-scale reconstruction | Zimmermann et al., 2021 |
| CarveME (Python) | Genome-scale reconstruction | Machado et al., 2018 |
| KBase (web application) | Genome-scale reconstruction and constraint-based modeling | Machado et al., 2018 |
| COBRApy (Python) | Constraint-based modeling | Ebrahim et al., 2013 |
| CellNetAnalyzer (Matlab) | Constraint-based modeling | von Kamp et al., 2017 |
| SteadyCom (Matlab) | Microbiome FBA | Chan et al., 2017 |
| MICOM (Python) | Microbiome FBA | Diener et al., 2020 |
| μBialSim (Matlab) | Microbiome dFBA | Popp and Centler, 2020 |
| SMETANA (command line) | Potential for cooperative and competitive interactions | Zelezniak et al., 2015 |
| GECKO (Matlab) | Enzyme-constrained modeling | Domenzain et al., 2022 |
| AutoPACMEN (Python, Matlab) | Enzyme-constrained modeling | Bekiaris and Klamt, 2020 |
| tINIT/ftINIT (Matlab) | Contextualization of genome-scale reconstructions | Gustafsson et al., 2023, Agren et al., 2014 |
| MEMOTE (command line) | Quality testing of constraint-based models | Lieven et al., 2020 |
| CobraMod (Python) | Curation of constraint-based models | Camborda et al., 2022 |