In Systems Biology, spatial modelling allows an accurate description of phenomena whose behaviour is influenced by the spatial arrangement of the elements. We present various modelling formalisms with spatial features, each using a different abstraction level of the real space.
The MIM Calculus, inspired by Molecular Interaction Maps (a graphical notation for bioregulatory networks) provides high-level operators with a direct biological meaning, which are used to describe the interaction capabilities of the elements of a system. The MIM calculus allows modelling compartments, therefore it allows distinguishing only the abstract position where an element is, identified by the name of the compartment. We also present a spatial extension to the membrane computing formalism P systems, in which membranes and objects are embedded in a two-dimensional discrete space. Some objects of a Spatial P system can be declared as mutually exclusive objects, with the constraint that each position can accommodate at most one of them. Finally, we present the Spatial Calculus of Looping Sequences (Spatial CLS), which is an extension of the Calculus of Looping Sequences (CLS), a formalism geared towards the modelling of cellular systems. In this case, models are based on two/three dimensional continuous space, and allow an accurate description of the motion of the elements, and of their size.