Abstract: A system and method of whole-cell process simulations may include: using at least one first hardware module, to produce a first predicted value, representing an expected behavior of a plurality of resource entities in a simulated biological cell; using at least one second hardware module, to produce a second predicted value, representing an interaction of a plurality of client entities with at least one of the plurality of resource entities in the simulated biological cell; using at least one third hardware module, to produce a third predicted value, representing an arbitration of interactions between the plurality of resource entities and the plurality of client entities in the simulated biological cell; and producing a simulated value of a product of a natural process in the simulated biological cell, based on said first, second and third predicted values.