Modelling Epigenetic Information Maintenance: A Kappa Tutorial

The purpose of this tutorial is to explain and illustrate an approach to the quantitative modelling of molecular interaction networks which departs from the usual notion of (bio-) chemical reaction. This tutorial is self-contained and supposes no familiarity with molecular biology. We shall use a modelling language called Kappa [1], but much of what we will present equally applies to the larger family of rule-based modelling frameworks -and in particular to the BNG language [2] which is very close to Kappa. For a technical exposition of Kappa as a stochastic graph rewriting system, the reader can consult Ref. [3]. To demonstrate the interest of a rule-based approach we will investigate a concrete biological question, that of the maintenance of epigenetic information. Our plan is to: propose in biological and informal terms a repair mechanism (§1) capture this mechanism into a simple rule-based model (§2) equip this rule set numerically (rule rates, copy numbers) to obtain a quantitative model (§3) Although the model we present here is congruent with the current evidence, and generates interesting results, it offers a -perhaps overlysimplified view of the relevant biological mechanisms. Its primary use is to introduce gradually the Kappa concepts and (some of its) methods in a concrete modelling situation, as we make progress in our plan.