Section: New Results

Avoiding stiffness in BioRica

Participants : David James Sherman [correspondant] , Joaquin Fernandez.

We previously formalized two strategies for integrating discrete control with continuous models, coefficient switches that control the parameters of the continuous model, and strong switches that choose different models [29] , [27] . While these strategies have proved useful for modeling hybrid systems in biotechnology [31] and medicine [28] , the resulting system model can be inefficient when the different subsystems evolve at very different time scales. In order to improve the efficiency of the resulting simulations, we investigated the use of Kofman's Quantized State Systems (QSS), and demonstrated that the QSS approach can be adapted to BioRica [13] . On the strength of this demonstration, we invited Joaquin Fernandez from Kofman's lab to Magnome. Joaquin had previously implemented an efficient library for QSS simulation, and during his stay succeeded in adapting it to our hybrid modeling framework. In his approach, SBML models with events are compiled into a hybrid model, using a variant of Modelica for surface syntax and using the QSS library for efficient simulation.