Table 3. Considered multilevel systems biology computational models against which the proposed model checking methodology and implementation were validated.
| M1 | M2 | M3 | M4 | |
|---|---|---|---|---|
| Description | Rat cardiovascular system dynamics | Uterine contractions of labour | Xenopus laevis cell cycle | Acute inflammation of the gut and lung |
| Model type | Deterministic | Deterministic | Hybrid | Stochastic |
| Modelling formalism(s) | Ordinary differential equations (ODE) | Cellular automata (CA) | ODEs + Cellular Potts model (CPM) | Agent based modelling (ABM) |
| Modelling software | JSim | Mathematica | Morpheus | NetLogo |
| Explicit spatial representation | N | Y | Y | Y |
| Levels of organization | Cellular + Organ system | Cellular + Tissue | Intracellular + Cellular | Cellular + Tissue + Organ |
| Case study reference | [13] | [14] | [15] | [16] |
| Model download link | http://virtualrat.org/sites/default/files/downloads/Workflow_Model_Files_12April2012.zip | http://s3-eu-west-1.amazonaws.com/files.figshare.com/1720626/Supporting_Information_S1 | http://imc.zih.tu-dresden.de/wiki/morpheus/doku.php?id=examples:multiscale#odes_in_cpm_cellscell_cycle_and_proliferation | http://bionetgen.org/SCAI-wiki/images/7/7d/GutLungAxis2.1.nlogo |
Each model (M1–M4) has an associated description and type (i.e. deterministic, stochastic or hybrid), was encoded using specific modelling formalisms and software, represents space explicitly or not (Y—Yes, N—No), spans different levels of organization, and has a corresponding reference paper and download link.