Benchmark-Models-PEtab
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Add reformulated Fiedler_BMCSystBiol2016
The authors used an identifiable, reformulated version of the model for Raf/MEK/ERK signaling after release from S-phase arrest:
The model for the relative phosphorylation levels does not depend explicitly on the total abundances $\text{[Raf}]_0$, $\text{[MEK}]_0$ and $\text{[ERK}]_0$ but only on products and ratios of these parameters with other parameters, e.g., $k_3\text{[Raf}]_0$. Defining these products and ratios as new parameters eliminates non-identifiabilities and reduces the number of parameters.
Compared to the existing implementation the state variables of the model are now the relative phosphorylation levels
$x_1 = \text{[pRaf] / [Raf}]_0, x_2 = \text{[pMEK] / [MEK}]_0, x_3 = \text{[pERK] / [ERK}]_0$.
Therefore, the PEtab observables are now $x2$ (pMEK_rel) and $x3$ (pERK_rel)
The interpretation of the scaling factors changes to the product of the scaling factor and $\text{[MEK}]_0$ for pMEK_rel, and the product of scaling factors and $\text{[ERK}]_0$ for pERK_rel.