Simbios Talk by Daniel Cook & John Gennari, University of Washington, September 12, 2007

Title: Biosimulation model reuse and reproducibility: A multi-scale example

In the field of biosimulation, there is a growing need for improved reproducibility and reuse of biosimulation models. Ideally, model reuse (or model adaptation) would span domains and scales, allowing biosimulation researchers to create larger, more richly detailed models than they would on their own. In our research, we have developed and tested a methodology and object-oriented systems analysis framework that allows for semi-automatic, multi-scale model integration. As part of this framework, we explicitly represent two sorts of declarative models: first, models of the biological systems, and second, the computational models that are derived from those systems. This approach allows researchers to build multiple computational models from a single biological model, and also to annotate explicitly the assumptions and simplifications of these models.

In this talk, we describe this representational framework and present a multi-scale use-case in the realm of cardiovascular regulation.  In particular, we describe three biosimulation models: (1) a cardiovascular fluid dynamics model, (2) a model of heart rate regulation by baroreceptor feedback, and (3) a cellular-level model of arteriolar smooth muscle contraction.  We demonstrate how our approach to annotating these models enables the merging of the three into a larger, multi-scale model that allows users to investigate physiological phenomena beyond the scope of the individual models.