Modelling, Simulation, and Tuning of Metabolic Networks Through Electronic Design Automation

This work presents an extended methodology that applies languages, techniques, and tools well established in the electronic design automation (EDA) field for modelling, simulation, and tuning of metabolic networks. The methodology, which has been implemented in an EDA-based platform, is compliant to modelling standards like SBML and Petri Nets (PN), and it allows for the automatic conversion of such model representations to an internal EDA description language. The platform requires the user to express system properties to be observed and to integrate the known experimental data into the system. As a result, the platform automatically extrapolates the system parametrization to reproduce, in a semi-quantitative way, the experimental results, to simulate the model under different conditions and, thus, to make easier the analysis of the dynamics that regulate the system. To evaluate both the feasibility and the performances, we applied the platform to model the purine metabolism and to reproduce the metabolomics data obtained from naive lymphocytes and autoreactive T cells implicated in the induction of experimental autoimmune disorders.