Significant advances are needed for food systems in terms of real-time prognosis capability developments, incorporating large scale modelling, distributed simulation and optimisation, and complete integration of the methods and algorithms. The goal is to be able to develop new paradigms at the frontier of life science and computing science for the management of systems like food systems. In parallel, just in the process of emerging and linked to these same questions is the science of complex systems, that proposes ways to understand systems located in turbulent, instable and changing environments. This paper points out and illustrates the interest to develop an approach adapting and coupling some fundamental tools of the complex system science. It combines viability and robustness analysis, multi-objective optimisation calculus and high computational performance using a computing grid. Adapted to the camembert cheese ripening, it has led to propose new strategies for control the process. One solution of the calculated pareto front, is compared to two trajectories tested during experiments led on a pilot, one standard and another optimized one. The total mass loss deviation for the calculated trajectory by comparison to the standard one is 0.04 kg in the same time and for identical microorganisms behaviour.