Some Petri Net reading

25 January 2010

Here are some reading indications for the material we have covered so far: Petri Nets, matrix representation, {T,P}-invariants, and the conversion to labelled transition systems.

Lecture notes set 1 and set 2 from a previous iteration of MLCSB cover these topics and include some extra examples.

Chapter 1 introduces and motivates biological modelling in general. Chapter 2 sections 2.1–2.3 describe Petri Nets; the remainder of Chapter 2 discusses representation in the Systems Biology Markup Language (SBML). Wilkinson does not cover logical and model-checking, but does treat probabilistic and stochastic models, which we shall return to later.

Heiner et al.
Sections 1–3 give an overview and some context to modelling in systems biology. Section 4 covers all the Petri Net material we have done so far, and in considerable depth. Read it to see just how detailed these analyses can get.

There are some accompanying slides from this summer school, which you may find helpful.