Section: New Results

Hierarchical modeling with BioRica

Participants : David James Sherman [correspondant] , Rodrigo Assar Cuevas, Nicolás Loira.

A recurring challenge for in silico modeling of cell behavior is that experimentally validated models are so focused in scope that it is difficult to repurpose them. Hierarchical modeling is one way of combining specific models into networks. Effective use of hierarchical models requires both formal definition of the semantics of such composition, and efficient simulation tools for exploring the large space of complex behaviors.

BioRica is a high-level hierarchical modeling framework for models combining continuous and discrete components. By providing a reliable and functional software tool backed by a rigorous semantics, we hope to advance real adoption of hierarchical modeling by the systems biology community. By providing an understandable and mathematically rigorous semantics, this will make is easier for practicing scientists to build practical and functional models of the systems they are studying, and concentrate their efforts on the system rather than on the tool.

Building on previous work that formalized strategies for integrating discrete control with continuous models, Rodrigo Assar defined a new framework for BioRica models using Kaufman's Quantized State Systems (in prep.).