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: 1. articulate in purely biological terms an epigenetic repair mechanism (§1); 2. capture this mechanism into a simple rule-based model (§2); 3. equip this rule set with numerical information (rule rates, copy numbers of various intervening agents) to obtain a quantitative model (§3.1-3.2); 4. exploit the said model by investigating various questions (§3.3-3.4). Although the model we present here is congruent with the current evidence, and generates interesting results, it offers a -perhaps overly- simplified 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.
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