and Beeman, 1998). There are also tools for modeling biochemical processes, e.g., E-CELL3 (Takahashi et al., 2004), STEPS (Wils and De Schutter, 2009; Hepburn et al., 2012), COPASI (Hoops et al., 2006), SBMLOdeSolver (Machné et al., 2006). The main challenge is to efficiently combine the modules by synchronizing the events properly at different time scales, by matching the spatial information into a topology or morphology, and by using optimization methods to computationally handle such massive amounts of data.
