Volume 56, Issue 2 - Special Issue: Petri Nets in the Biosciences / Ina Koch, Wolfgang Reisig and Falk Schreiber

The reconstruction of models from experimental data is a challenging problem due to the inherited complexity of the studied biological systems. We discuss an exact, exclusively data-driven approach to reconstruct Petri nets, a framework which turned out to coherently model static interactions and dynamic processes. The reconstructed models shall reproduce the experimentally observed dynamic behavior in a simulation. For that, we consider Petri nets with two types of extensions, priority relations among the transitions and control-arcs, to obtain additional activation rules that control the dynamic behavior. Here, we give an overview on results concerning the reconstruction of standard networks with and without priorities, extended Petri nets, and extended Petri nets with priorities. All these approaches aim at reconstructing all networks of the studied type that fit the given experimental data, to provide all possible alternatives of mechanisms behind the experimentally observed phenomena.

A Petri net library, called PNlib, is presented to enable graphical hierarchical modeling, hybrid simulation and animation of processes in life sciences among others. In order to model these processes, a powerful and universally usable mathematical modeling concept – xHPN (extended Hybrid Petri Nets) – has been established. This formalism is used as specification for the PNlib realized by the object-oriented modeling language Modelica. The PNlib is freely available and can be downloaded on the Modelica homepage www.modelica.org/libraries.

Characterizing the dynamics of cellular signaling pathways with external simuli or drug treatment is critical for the understanding of mechanisms of cellular behavors. Petri Net, as a non-parametric approach, has been widely used for studying dynamics of a large scale of signaling network only based on the connections (interactions) within this network. In this article, we will describe an extension of the Petri net methods, called Enhanced Petri Net (EPN), specifcally designed for analyzing and modeling the dynamics of signaling pathways in order to predict the unknown signaling mechanisms of targeted-therapy drugs.

Petri net methodology has been widely used for modeling and simulation of biological systems due to its intuitive graphical representation and mathematical power for concurrent systems. In this article, some of the major problems arising in this field are addressed, ongoing progresses are discussed, and possible solutions are suggested.

Two features distinguish Java from other main-stream programming languages like C and C++: its built-in support for concurrency and safety guarantees such as type safety or safe execution in a sandbox. In this work, we build a formal, unified model of Java concurrency, validate it empirically, and analyse it with respect to the safety guarantees using a proof assistant. We show that type safety and Java's data race freedom guarantee hold. Our analysis, however, revealed a weakness in the Java security architecture, because the Java memory model theoretically allows pointer forgery. As a result, this work clarifies the specification of the Java memory model.