http://user.it.uu.se/~jarst116/slides/week4.pdf

Graph-Based Algorithms for Boolean Function Manipulation

We launch the new probabilistic model checker Storm. It features the analysis of discrete- and continuous-time variants of both Markov chains and MDPs. It supports the Prism and JANI modeling languages, probabilistic programs, dynamic fault trees and generalized stochastic Petri nets. It has a modular set-up in which solvers and symbolic engines can easily be exchanged. It offers a Python API for rapid prototyping by encapsulating Storm’s fast and scalable algorithms. Experiments on a variety of benchmarks show its competitive performance.

A Storm is Coming: A Modern Probabilistic Model Checker

We give a description of a Petri net-based framework for modelling and analysing biochemical pathways, which unifies the qualitative, stochastic and continuous paradigms. Each perspective adds its contribution 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 qualitative descriptions are abstractions over stochastic or continuous descriptions, 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.

/pdf/petri-nets-for-systems-and-synthetic-biology-2phlqoy7lg.pdf

Petri nets for systems and synthetic biology

The tool Snoopy provides a unifying Petri net framework which has particularly many application scenarios in systems and synthetic biology. The framework consists of two levels: uncoloured and coloured. Each level comprises a family of related Petri net classes, sharing structure, but being specialized by their kinetic information. Petri nets of all net classes within one level can be converted into each other, while changing the level involves user-guided folding or automatic unfolding. Models can be hierarchically structured, allowing for the mastering of larger networks. Snoopy supports the simultaneous use of several Petri net classes; the graphical user interface adapts dynamically to the active one. Built-in animation and simulation (depending on the net class) are complemented by export to various analysis tools. Snoopy facilitates the extension by new Petri net classes thanks to its generic design.

Snoopy --- a unifying petri net tool

Interactive, distributed, and embedded systems often behave stochastically, for example, when inputs, message delays, or failures conform to a probability distribution. However, reasoning analytically about the behavior of complex stochastic systems is generally infeasible. While simulations of systems are commonly used in engineering practice, they have not traditionally been used to reason about formal specifications. Statistical model checking (SMC) addresses this weakness by using a simulation-based approach to reason about precise properties specified in a stochastic temporal logic. A specification for a communication system may state that within some time bound, the probability that the number of messages in a queue will be greater than 5 must be less than 0.01. Using SMC, executions of a stochastic system are first sampled, after which statistical techniques are applied to determine whether such a property holds. While the output of sample-based methods are not always correct, statistical inference can quantify the confidence in the result produced. In effect, SMC provides a more widely applicable and scalable alternative to analysis of properties of stochastic systems using numerical and symbolic methods. SMC techniques have been successfully applied to analyze systems with large state spaces in areas such as computer networking, security, and systems biology. In this article, we survey SMC algorithms, techniques, and tools, while emphasizing current limitations and tradeoffs between precision and scalability.

https://dl.acm.org/doi/pdf/10.1145/3158668

A Survey of Statistical Model Checking

MARCIE is a tool for the analysis of generalized stochastic Petri nets which can be augmented by rewards. The supported analysis methods range from qualitative and quantitative standard properties to model checking of established temporal logics. MARCIE's analysis engines for bounded Petri net models are based on Interval Decision Diagrams. They are complemented by simulative and approximative engines to allow for quantitative reasoning on unbounded models. Most of the quantitative analyses benefit from a multi-threaded implementation. This paper gives an overview on MARCIE's functionality and architecture and reports on the recently added feature of CSRL and PLTLc model checking.

MARCIE: model checking and reachability analysis done efficiently

MARCIE is a multi-threaded tool for the analysis of Generalized Stochastic Petri Nets. Its capabilities range from standard properties of qualitative Petri nets to CTL and CSL model checking, recently extended by rewards. The core of MARCIE builds upon Interval Decision Diagrams for the symbolic representation of marking sets of bounded Petri nets (finite state space) and on-the-fly matrix computation for numerical analysis. Approximative engines supporting fast adaptive uniformization and Gillespie simulation open the door to quantitative reasoning on unbounded Petri nets (infinite state space). This paper presents MARCIE's architecture and its most important distinguishing features. Extensive computational experiments demonstrate MARCIE''s strength in comparison with related tools.

https://www-dssz.informatik.tu-cottbus.de/publications/slides/2013_petrinets_marcie_sld.pdf

MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly

Charlie is an extensible thread-based Java tool for analysing Petri nets. Its built-in functionalities apply standard analysis techniques of Petri net theory (e.g. invariants, siphon/trap property) to determine structural and behavioural properties of place/transition Petri nets, complemented by explicit CTL and LTL model checking. Charlie comes with a plugin mechanism, which permits to easily extend its basic functionality as it has been demonstrated for, e.g., structural reduction and time-dependent Petri nets. Charlie’s primary focus is teaching. For thispurpose, it has a rule system comprising standard theorems of Petri net theory to possibly decide further properties based on the already determined ones. All applied rules are reported by default, so the user may keep track of all analysis steps. The tool is in use for model verification of technical systems, especially software-based systems, as well as for model validation of natural systems, i.e. biochemical networks, such as metabolic, signal transduction, and gene regulatory networks. It is publicly available at http://www-dssz.informatik.tu-cottbus.de/DSSZ/Software/Charlie.

https://www-dssz.informatik.tu-cottbus.de/publications/slides/2015_06_charlie-petrinet2015.sld.pdf

Charlie – An Extensible Petri Net Analysis Tool

This paper presents an Interval Decision Diagram based approach to symbolic CSL model checking of Continuous Time Markov Chains which are derived from stochastic Petri nets. Matrix-vector and vector-matrix multiplication are the major tasks of exact analysis. We introduce a simple, but powerful algorithm which uses explicitly the Petri net structure and allows for parallelisation. We present results demonstrating the efficiency of our first prototype implementation when applied to biochemical network models, specifically with increasing token numbers. Our tool currently supports CSL model checking of time-bounded operators and the Next operator for ordinary stochastic Petri nets.

/pdf/csl-model-checking-of-biochemical-networks-with-interval-467703fwgk.pdf

Martin Schwarick

Papers

Snoopy --- a unifying petri net tool

MARCIE: model checking and reachability analysis done efficiently

MARCIE - Model Checking and Reachability Analysis Done EffiCIEntly

Charlie – An Extensible Petri Net Analysis Tool

CSL Model Checking of Biochemical Networks with Interval Decision Diagrams