Ioana Cristescu (Department of Systems Biology, Harvard Medical School, Boston, USA) |
Walter Fontana (Department of Systems Biology, Harvard Medical School, Boston, USA) |
Jean Krivine (IRIF, CNRS and Paris Diderot University) |
Graph rewrite formalisms are a powerful approach to modeling complex molecular systems. They capture the intrinsic concurrency of molecular interactions, thereby enabling a formal notion of mechanism (a partially ordered set of events) that explains how a system achieves a particular outcome given a set of rewrite rules. It is then useful to verify whether the mechanisms that emerge from a given model comply with empirical observations about their mutual interference. In this work, our objective is to determine whether a specific event in the mechanism for achieving X prevents or promotes the occurrence of a specific event in the mechanism for achieving Y. Such checks might also be used to hypothesize rules that would bring model mechanisms in compliance with observations. We define a rigorous framework for defining the concept of interference (positive or negative) between mechanisms induced by a system of graph-rewrite rules and for establishing whether an asserted influence can be realized given two mechanisms as an input. |
ArXived at: https://dx.doi.org/10.4204/EPTCS.286.6 | bibtex | |
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