Non local causality analysis in rule-based models

CMACS workshop NYC 2012 " Programs as models " project Import tools from theoretical computer science in order to describe and analyze biological systems Develop new technique to cope with the complexity of the cell Theoretical computer science Abstract interpretation Concurrency theory Abstract. Modelling is becoming a necessity in studying biological signalling pathways, because the combinatorial complexity of such systems rapidly overwhelms intuitive and qualitative forms of reasoning. Yet, this same combinatorial explosion makes the traditional modelling paradigm based on systems of dierential equations impractical. In contrast, agent-based or concurrent languages, such as [1–3] or the closely related BioNetGen language [4–10], describe biological interactions in terms of rules, thereby avoiding the combinatorial explosion besetting dierential equations. Rules are expressed in an intuitive graphical form that trans