With modern computational power and parallelization support , it is technically no longer a problem to assemble and simulate systems of thousands of equations, yet we face more fundamental difficulties devising a useful simulation of all processes inside an E. coli cell. Whereas a simulation of engine combustion is based on a few, rather simple, equations, describing for example, continuity, energy and momentum , there are no universal equations describing the single cellular processes. Every enzymatic reaction and every transcription factor binding process must be described by some equation that needs to be experimentally validated and parameterised with tedious, time-consuming and usually manual experiments. Unfortunately, production of new, high-throughput data collections by individual labs will not solve all challenges that hinder development of powerful predictive models. For once, we require extensive standardisation which has been proven to be key in other engineering fields. However,despite community awareness and excellent, coherent efforts , until now standardization is unfortunately still not a priority for academic research, nor funding agencies . Additionally, when simulating biological systems one has to face uncertainties on two levels: Like in complex physical systems, the complexity alone will bring forth emergent, and intrinsically unpredictable, properties. In addition to that, the single entities that make up the biological system are only approximately characterised and often their behaviour is not fully explained by an underlying theory.