How do we think about natural phenomenon to formalize them in a programming languageSomogyi Endre, James Sluka and James A. Glazier. “Formalizing Knowledge in Multi-Scale Agent-Based Simulations” Proceedings of the ACM/IEEE 19th International Conference on Model Driven Engineering Languages and Systems. ACM, 2016.
The JIT compiler, simulation and analysis library for SBML chemical reaction networks that I developed as part of my PhD thesis, this work combined with my previous work on mass-spring physically based simulation is the basis of Mechanica.Somogyi, Endre, Jean-Marie Bouteiller, James A. Glazier, Matthias König, J. Kyle Medley, Maciej H. Swat, and Herbert M. Sauro. “libRoadRunner: a high performance SBML simulation and analysis library” Bioinformatics(2015): btv363