Table 1. Wnt simulation models (as of Feb. 1, 2021) with those included in this study printed in bold.
| Study | BioModels | MA | SA | Scale | Add. Compartm. | Add. Pathways/Models |
|---|---|---|---|---|---|---|
| [28] | ✓ | ODE | det | SC | − | − |
| [29] | − | ODE | det | SC | − | − |
| [30] | − | ODE | det | SC | − | − |
| [31] | − | PDE | det | TOL | − | − |
| [32] | ✓ | ODE | det | SC | Nuc | MAPK/ERK |
| [33] | − | ODE | det | SC | − | Notch |
| [34] | ✓ | ODE | det | SC | − | − |
| [35] | − | ODE | det | SC | − | − |
| [36] | ✓ | ODE | det | SC | Nuc | Notch, MAPK/ERK |
| [37] | − | PDE | det&stoch | MC | − | E-cadherin |
| [38] | − | ODE | det | SC | − | − |
| [39] | − | ODE | det&stoch | MC | − | Cell cycle, E-cadherin |
| [40] | − | ODE | det | SC | − | − |
| [41] | − | ODE | det | SC | − | − |
| [42] | − | PDE | stoch | MC | − | − |
| [43] | − | ODE | det | SC | − | MAPK/ERK |
| [44] | − | PDE | det&stoch | MC | − | Notch |
| [45] | − | ODE | det | SC | − | − |
| [46] | ✓ | Rule | det&stoch | SC | Nuc | Cell cycle |
| [47] | − | ODE | det | SC | Nuc | − |
| [48] | − | ODE | det | SC | Nuc | Notch |
| [49] | − | ODE | stoch | SC | Nuc, GA | E-cadherin |
| [50] | − | ODE | det | SC | Nuc | − |
| [51] | − | Rule | stoch | SC | Nuc, Mem, LR | ROS |
| [52] | − | ODE | det | SC | Nuc | − |
| [53] | ✓ | ODE | det | SC | − | MAPK/ERK, PI3K/Akt |
| [54] | − | Bool | det | SC | − | PI3K/AKT, MAPK/ERK, Rho/Rac |
| [55] | − | ODE | det | SC | − | − |
| [56] | − | Rule | det | SC | Nuc, End, Mem, LR | − |
| [57] | − | Rule | stoch | SC | Nuc | ROS |
| [58] | − | ODE | det&stoch | MC | − | Cell cycle, Hippo |
A list of published simulation studies of the Wnt signaling pathway is presented showing the references, the availability of the simulation models in BioModels, the modeling approaches (MA), the simulation approaches (SA), the scale of the models, additional compartments as well as additional pathways or sub-models included. The authors of the studies printed in bold are: [28]: Lee et al. (2003), [29]: Krüger and Heinrich (2004), [30]: Cho et al. (2006), [31]: Sick et al. (2006), [32]: Kim et al. (2007), [33]: Rodríguez-González et al. (2007), [34]: van Leeuwen et al. (2007), [35]: Wawra et al. (2007), [36]: Goldbeter and Pourquié (2008), [39] van Leeuwen et al. (2009), [41]: Mirams et al. (2010), [45]: Kogan et al. (2012), [46]: Mazemondet et al. (2012), [48]: Wang et al. (2013), [49]: Chen et al. (2014), [51]: Haack et al. (2015), [53]: Padala et al. (2017), [56]: Haack et al. (2020), and [57]: Staehlke et al. (2020). The BioModels IDs of the simulation models available in BioModels are: [28]: BIOMD0000000658, [32]: BIOMD0000000149, [34]: MODEL2001090001, [36]: BIOMD0000000201, [46]: MODEL1303140000, [53]: BIOMD0000000648. The modeling approaches (MA) are: ODE-based (ODE), PDE-based (PDE), rule-based or reaction-based (Rule), and Boolean network model (Bool). The simulation approaches (SA) are: det (deterministic), stoch (stochastic). The scale may be single cell (SC), multi cell (MC) or at a more abstract tissue/organ level (TOL). Every simulation model contains at least one compartment—usually the cytosol. We also denote additional compartments where reactions may take place and where some species may shuttle into or out of: Nucleus (Nuc), Membrane (Mem), Endosome (End), Golgi apparatus (GA), Lipid Raft (LR). Models without shuttling are considered to have only one compartment even though they describe processes in different places, for example, in the cytosol, nucleus and at the cell membrane.