1,966 research outputs found
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
A Polynomial Translation of pi-calculus FCPs to Safe Petri Nets
We develop a polynomial translation from finite control pi-calculus processes
to safe low-level Petri nets. To our knowledge, this is the first such
translation. It is natural in that there is a close correspondence between the
control flows, enjoys a bisimulation result, and is suitable for practical
model checking.Comment: To appear in special issue on best papers of CONCUR'12 of Logical
Methods in Computer Scienc
A Forward Reachability Algorithm for Bounded Timed-Arc Petri Nets
Timed-arc Petri nets (TAPN) are a well-known time extension of the Petri net
model and several translations to networks of timed automata have been proposed
for this model. We present a direct, DBM-based algorithm for forward
reachability analysis of bounded TAPNs extended with transport arcs, inhibitor
arcs and age invariants. We also give a complete proof of its correctness,
including reduction techniques based on symmetries and extrapolation. Finally,
we augment the algorithm with a novel state-space reduction technique
introducing a monotonic ordering on markings and prove its soundness even in
the presence of monotonicity-breaking features like age invariants and
inhibitor arcs. We implement the algorithm within the model-checker TAPAAL and
the experimental results document an encouraging performance compared to
verification approaches that translate TAPN models to UPPAAL timed automata.Comment: In Proceedings SSV 2012, arXiv:1211.587
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Computer-aided analysis of concurrent systems
The introduction of concurrency into programs has added to the complexity of the software design process. This is most evident in the design of communications protocols where concurrency is inherent to the behavior of the system. The complexity exhibited by such software systems makes more evident the needs for computer-aided tools for automatically analyzing behavior.The Distributed Systems project at UCI has been developing a suite of tools, based on Petri nets, which support the design and evaluation of concurrent software systems. This paper focuses attention on one of the tools: the reachability graph analyzer (RGA). This tool provides mechanisms for proving general system properties (e.g., deadlock-freeness) as well as system-specific properties. The tool is sufficiently general to allow a user to apply complex user-defined analysis algorithms to reachability graphs. The alternating-bit protocol with a bounded channel is used to demonstrate the power of the tool and to point to future extensions
Generic Pipelined Processor Modeling and High Performance Cycle-Accurate Simulator Generation
Detailed modeling of processors and high performance cycle-accurate
simulators are essential for today's hardware and software design. These
problems are challenging enough by themselves and have seen many previous
research efforts. Addressing both simultaneously is even more challenging, with
many existing approaches focusing on one over another. In this paper, we
propose the Reduced Colored Petri Net (RCPN) model that has two advantages:
first, it offers a very simple and intuitive way of modeling pipelined
processors; second, it can generate high performance cycle-accurate simulators.
RCPN benefits from all the useful features of Colored Petri Nets without
suffering from their exponential growth in complexity. RCPN processor models
are very intuitive since they are a mirror image of the processor pipeline
block diagram. Furthermore, in our experiments on the generated cycle-accurate
simulators for XScale and StrongArm processor models, we achieved an order of
magnitude (~15 times) speedup over the popular SimpleScalar ARM simulator.Comment: Submitted on behalf of EDAA (http://www.edaa.com/
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RGA users manual : version 2.3
RGA is an interpreter for a special language designed for the analysis of reachability graphs, or control flow graphs, generated from Petri nets. Although in some cases the reachability graph can become too large to be tractable, or can even be infinite, many interesting problems exist whose reachability graphs are of reasonable size. In RGA, the user has access to the names of the places in the net, and to the states of the reachability graph. The structure of the graph is also available through functions which return the sets of successor or predecessor states of a state and the transition-firings connecting the states. The RGA language allows dynamic typing of identifiers, recursion, and function and operator overloading. Rather than providing a number of predefined analysis functions, RGA provides primitive functions which allow the user to conduct complex analyses with little programming effort. RGA is part of a suite of tools, called P-NUT, intended to facilitate the analysis of concurrent systems described by Petri nets
Read Operators and their Expressiveness in Process Algebras
We study two different ways to enhance PAFAS, a process algebra for modelling
asynchronous timed concurrent systems, with non-blocking reading actions. We
first add reading in the form of a read-action prefix operator. This operator
is very flexible, but its somewhat complex semantics requires two types of
transition relations. We also present a read-set prefix operator with a simpler
semantics, but with syntactic restrictions. We discuss the expressiveness of
read prefixes; in particular, we compare them to read-arcs in Petri nets and
justify the simple semantics of the second variant by showing that its
processes can be translated into processes of the first with timed-bisimilar
behaviour. It is still an open problem whether the first algebra is more
expressive than the second; we give a number of laws that are interesting in
their own right, and can help to find a backward translation.Comment: In Proceedings EXPRESS 2011, arXiv:1108.407
Encoding Higher Level Extensions of Petri Nets in Answer Set Programming
Answering realistic questions about biological systems and pathways similar
to the ones used by text books to test understanding of students about
biological systems is one of our long term research goals. Often these
questions require simulation based reasoning. To answer such questions, we need
formalisms to build pathway models, add extensions, simulate, and reason with
them. We chose Petri Nets and Answer Set Programming (ASP) as suitable
formalisms, since Petri Net models are similar to biological pathway diagrams;
and ASP provides easy extension and strong reasoning abilities. We found that
certain aspects of biological pathways, such as locations and substance types,
cannot be represented succinctly using regular Petri Nets. As a result, we need
higher level constructs like colored tokens. In this paper, we show how Petri
Nets with colored tokens can be encoded in ASP in an intuitive manner, how
additional Petri Net extensions can be added by making small code changes, and
how this work furthers our long term research goals. Our approach can be
adapted to other domains with similar modeling needs
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