Schematic description of the example model. The example model comprises three distinct hierarchical levels. At the bottom level, interacting proteins describe the inctracellular dynamics of a fission yeast cell (reactions 1-5). The molecular species and reactions are similar to those described in . The intermediate level describes dynamics of entire cell states, i.e. cell growth (6), cell cycle phase transitions (7-9), and division including mating type switching (9). In addition, cells may secrete pheromone molecules (P-factor and M-factor) to the extracellular medium (10). Various inter-level causalities between the intermediate and the bottom level influence processes both in an upward (7-9) and downward causation manner (4,11-12). The top level discretizes the environment of cells into multiple fictive compartments in order to study spatial dynamics of pheromone diffusion and displacement of cells (13-14). Abbreviations used for naming the species in the model: Y (cyclin), YP (phosphorylated cyclin), D (cdc2), MI (inactive MPF), MA (active MPF), C (fission yeast cell), FP (P-factor pheromone), FM (M-factor pheromone), G (voxel of spatial grid).
Maus et al. BMC Systems Biology 2011 5:166 doi:10.1186/1752-0509-5-166