Table 1.
Deterministic models developed to understand cell-free.
| Modeling strategy | Problems tackled | Level of detail | Description | Strength | Weakness | References |
|---|---|---|---|---|---|---|
| ODE | Protein production in cell-free | Simple* | Michaelis-Menten for the translation processes, as well as for degradation | Simple, quantitative | Parameters values are experiment dependent | Karzbrun et al., 2011 |
| ODE | Protein production in cell-free | Simple* | Simple description of the transcription and translation processes. One parameter summarize each | Simple, qualitative | Parameters values are experiment dependent | Stögbauer et al., 2012; Siegal-Gaskins et al., 2014 |
| ODE | Protein production in cell-free Resource competition in cell-free | Complex* | Detailed modeling: Particular focus on the translation process and the competition for the translation machinery | Generalization power quantitative | Parameters values are experiment dependent | Underwood et al., 2005; Borkowski et al., 2018 |
| ODE | Protein production in cell-free Resource competition in cell-free | Simple* | Binding, unbinding and elongation bundled in one parameter. Accounts for number of RNAP, ribosomes, and promoter/RBS strengths | Easily adaptable to a new situation or phenomena | Necessitates parameter determination for new situation | Gyorgy and Murray, 2016; Halter et al., 2018; Voyvodic et al., 2018 |
| ODE | Protein production in cell-free Resource depletion in cell-free | Complex* | Accounts for all known processes, including NTP consumption and degradation | Models biochemical phenonema precisely so generalisable | Important parameter identification/estimation needed | Siegal-Gaskins et al., 2013; Tuza et al., 2013; Nieß et al., 2017; Matsuura et al., 2018; Moore et al., 2018 |
| Constraint based | Protein production with cell-free Metabolism in cell-free | Complex* | Modification of E. Coli metabolic model to account for cell-free constraints | Accounts for the full metabolism, can use constraints based methods such as FBA | Defining the objectives, require deeper knowledge of reactions in cell-free | Vilkhovoy et al., 2018 |
*
Simple stands for one protein produced and limited amount of parameters (< 10) Complex stands for more than one protein produced or/and large amount of parameters (more than 10).