Petri nets for systems and synthetic biology

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which uni¯es the qualita- tive, stochastic and continuous paradigms. Each perspective adds its con- tribution to the understanding of the system, thus the three approaches do not compete, but complement each other. We illustrate our approach by applying it to an extended model of the three stage cascade, which forms the core of the ERK signal transduction pathway. Consequently our focus is on transient behaviour analysis. We demonstrate how quali- tative descriptions are abstractions over stochastic or continuous descrip- tions, and show that the stochastic and continuous models approximate each other. Although our framework is based on Petri nets, it can be applied more widely to other formalisms which are used to model and analyse biochemical networks

Partial Orders for Efficient BMC of Concurrent Software

This version previously deposited at arXiv:1301.1629v1 [cs.LO]The vast number of interleavings that a concurrent program can have is typically identified as the root cause of the difficulty of automatic analysis of concurrent software. Weak memory is generally believed to make this problem even harder. We address both issues by modelling programs' executions with partial orders rather than the interleaving semantics (SC). We implemented a software analysis tool based on these ideas. It scales to programs of sufficient size to achieve first-time formal verification of non-trivial concurrent systems code over a wide range of models, including SC, Intel x86 and IBM Power

A Reduced Semantics for Deciding Trace Equivalence

Many privacy-type properties of security protocols can be modelled using trace equivalence properties in suitable process algebras. It has been shown that such properties can be decided for interesting classes of finite processes (i.e., without replication) by means of symbolic execution and constraint solving. However, this does not suffice to obtain practical tools. Current prototypes suffer from a classical combinatorial explosion problem caused by the exploration of many interleavings in the behaviour of processes. M\"odersheim et al. have tackled this problem for reachability properties using partial order reduction techniques. We revisit their work, generalize it and adapt it for equivalence checking. We obtain an optimisation in the form of a reduced symbolic semantics that eliminates redundant interleavings on the fly. The obtained partial order reduction technique has been integrated in a tool called APTE. We conducted complete benchmarks showing dramatic improvements.Comment: Accepted for publication in LMC