Table 2.
Comparison of some tools and frameworks for GSM-based modelling of interactions in communities. BU: 'bottom-up' i.e. association of individual GSMs into small communities. TD: 'top-down' i.e. analyses starting from large metagenomic-identified communities.
| Tool/Framework | Modelling | Application | Approach |
|---|---|---|---|
| DMMM [152] | dynamic steady-state | a community of 2 bacteria | BU |
| OptCom [147] | steady-state | multi-objective optimisation of communities from 2 to 4 species | BU |
| dOptCom [153] | dynamic steady-state | multi-objective & multi-level optimisation of 3-species communities | BU |
| CASINO [170] | steady-state | 6-species communities | BU |
| COMETS [154] | dynamic steady-state + spatial | 2 and 3-species communities | BU |
| BacArena [155] | dynamic steady-state + spatial | 7-species community | BU |
| SteadyCom [149] | steady-state | 4 and 9-species communities | BU |
| Greenblum et al 2012 [128] | topological | ‘bag-of-genes' per sample | TD |
| Metage2Metabo [164] | network expansion | de novo GSM reconstruction, global analyses and community reduction | TD |
| MMinte [117] | steady-state | pairwise analyses and interactions | TD |
| MICOM [161] | steady-state | metagenomic samples mapped to existing GSMs or newly reconstructed GSMs drafts from genomes following OTUs alignment | TD |