Techniques for modeling living biological systems include receiving constant values for multiple interaction factors wij. A set of initial state values is received for state variables that indicate relevant properties of a living biological system. Also received is a set of trial values for perturbation variables that indicate factors that might affect one or more of the relevant properties of the biological system. A temporal change in a value for a particular state variable is determined based on a non-linear transformation of a sum of the trial value for the perturbation that affects the particular state added to a sum of all non-zero values for a product of wij and a state variable over all state variables.In some embodiments, measurement-based values are received for a measurable subset of the state variables. Values for the constant interaction factors wij are determined based on the measurement-based values.