In this area, Mathomics states alliances for the reconstruction of metabolic and gene regulatory networks, starting either from a genome annotation (ideally from an annotation produced within the group), transcriptomic data or metabolomic data. Integration tools can be also developed and applied. Based on the reconstruction, dynamic and stationary models of a biological system can be generated. Particularly, models for flux balance analysis of the metabolism of the studied organisms at different scales (even reaching genome scale if necessary) can be developed. These models are oriented towards stationary simulation of metabolism and can be enriched with real measurements of fluxes. Thermodynamics of the different reactions can also be used to impose further boundaries to the stationary models of the studied metabolism. This kind of modeling delivers relevant advice on the strategies to follow in both genetic and media modifications, oriented to maximize a desired phenotypic behavior of the studied organisms. Furthermore, Mathomics can provide the required mathematical analysis of the equilibrium states of the biological networks under study and the analysis of the critical parameters of the models.