lpNet: a linear programming approach to reconstruct signal transduction networks. - Marta R. A. Matos; Bettina Knapp; Lars Kaderali (Bioinform., 2015)

yaml2sbml: Human-readable and -writable specification of ODE models and their conversion to SBML. - Jakob Vanhoefer; Marta R. A. Matos; Dilan Pathirana; Yannik Schälte; Jan Hasenauer (J. Open Source Softw., 2021)