Table 2.
Summary of the case studies. Each column describes a calibration problem. Further details can be found in Additional file 3 (numerical data) and Additional file 4 (detailed descriptions including the model differential equations)
| Short name | BBG | FHN | MAPK | GOsc | TGFB | TSMP | CHM |
|---|---|---|---|---|---|---|---|
| Description | Biomass | FitzHugh- | MAPK | Goodwin’s | TGF- β | 3-Step | Chemotaxis |
| Batch | Nagumo | Signalling | Oscillator | Signalling | Metabolic | Signalling | |
| Growth | Oscillator | Pathway | Pathway | Pathway | Pathway | ||
| Reference | [123] | [124, 125] | [126] | [127] | [48] | [44] | [128] |
| Implementation of dynamics | [123] | BIOMD00000000010 ∗ | BIOMD00000000346 ∗, [129] | [130] | [48] | [44] | BIOMD00000000404 ∗ |
| Total parameters | 4 | 3 | 22 | 8 | 21 | 36 | 60 |
| Estimated parameters | 4 | 3 | 6 | 8 | 18 | 36 | 38 |
| States | 2 | 2 | 8 | 3 | 18 | 8 | 26 |
| Observed states | 2 | 1 | 2 | 3 | 16 | 8 | 7(+1) |
| Experiments | 1 | 1 | 1 | 1 | 1 | 8 | 2 |
| Data points | 22 | 6 | 20 | 20 | 240 | 1344 | 160 |
*The dynamic model can be found in the Biomodels Database (http://www.ebi.ac.uk/biomodels-main)