||Feb 6, 2015
||Analyzing regulation thanks to a concurrent dynamic framework: the Process Hitting
Regulation is a key aspect of biological systems, all the way from the molecular scale to the ecological scale. In order to make relevant analyzes of such systems, it is then crucial to get a precise understanding of this phenomenon.The modeling of biological regulation can be divided into two main trends. The first is based on ordinary differential equations involving the quantitative expression of the interacting components. However, as data in a biological context are often more qualitative than quantitative, it is meaningful that another trend, based on qualitative modeling, emerged: Boolean paradigms may appear to be simplified models, but they led to significant results about the behavior of networks, such as cyclicity or steady states. Moreover, these models have been extended over the years, for example, to consider additional levels of expressions.
Nevertheless, classical analysis approaches of these models suffer from the inherent combinatorial explosion of the state space. As a result, it is generally difficult to address systems with more than ten interacting components. In such a context, it is crucial to identify subclasses of existing frameworks that are both expressive and simple enough to design efficient analysis approaches.
In order to address this scalability issue, we introduced a new modeling framework, called Process Hitting. Establishing relationships between the components at the most atomic level possible, the Process Hitting opens the way to many static analysis and abstract interpretation methods to study complex dynamic properties.
In this talk, we will present the Process Hitting modeling approach and the methods we designed to analyze its dynamics. We will illustrate its benefits on a case study and give some benchmarks.