2,822 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 Logic for Constraint-based Security Protocol Analysis
We propose PS-LTL, a pure-past security linear temporal logic that allows the specification of a variety of authentication, secrecy and data freshness properties. Furthermore, we present a sound and complete decision procedure to establish the validity of security properties for symbolic execution traces, and show the integration with constraint-based analysis techniques
Parameterized Synthesis Case Study: AMBA AHB (extended version)
We revisit the AMBA AHB case study that has been used as a benchmark for
several reactive syn- thesis tools. Synthesizing AMBA AHB implementations that
can serve a large number of masters is still a difficult problem. We
demonstrate how to use parameterized synthesis in token rings to obtain an
implementation for a component that serves a single master, and can be arranged
in a ring of arbitrarily many components. We describe new tricks -- property
decompositional synthesis, and direct encoding of simple GR(1) -- that together
with previously described optimizations allowed us to synthesize the model with
14 states in 30 minutes.Comment: Moved to appendix some not very important proofs. To section
'optimizations: added the model for 0-process. Extended version of the paper
submitted to SYNT 201
A Logic for True Concurrency
We propose a logic for true concurrency whose formulae predicate about events
in computations and their causal dependencies. The induced logical equivalence
is hereditary history preserving bisimilarity, and fragments of the logic can
be identified which correspond to other true concurrent behavioural
equivalences in the literature: step, pomset and history preserving
bisimilarity. Standard Hennessy-Milner logic, and thus (interleaving)
bisimilarity, is also recovered as a fragment. We also propose an extension of
the logic with fixpoint operators, thus allowing to describe causal and
concurrency properties of infinite computations. We believe that this work
contributes to a rational presentation of the true concurrent spectrum and to a
deeper understanding of the relations between the involved behavioural
equivalences.Comment: 31 pages, a preliminary version appeared in CONCUR 201
Automated Synthesis of Distributed Self-Stabilizing Protocols
In this paper, we introduce an SMT-based method that automatically
synthesizes a distributed self-stabilizing protocol from a given high-level
specification and network topology. Unlike existing approaches, where synthesis
algorithms require the explicit description of the set of legitimate states,
our technique only needs the temporal behavior of the protocol. We extend our
approach to synthesize ideal-stabilizing protocols, where every state is
legitimate. We also extend our technique to synthesize monotonic-stabilizing
protocols, where during recovery, each process can execute an most once one
action. Our proposed methods are fully implemented and we report successful
synthesis of well-known protocols such as Dijkstra's token ring, a
self-stabilizing version of Raymond's mutual exclusion algorithm,
ideal-stabilizing leader election and local mutual exclusion, as well as
monotonic-stabilizing maximal independent set and distributed Grundy coloring
On Formal Methods for Collective Adaptive System Engineering. {Scalable Approximated, Spatial} Analysis Techniques. Extended Abstract
In this extended abstract a view on the role of Formal Methods in System
Engineering is briefly presented. Then two examples of useful analysis
techniques based on solid mathematical theories are discussed as well as the
software tools which have been built for supporting such techniques. The first
technique is Scalable Approximated Population DTMC Model-checking. The second
one is Spatial Model-checking for Closure Spaces. Both techniques have been
developed in the context of the EU funded project QUANTICOL.Comment: In Proceedings FORECAST 2016, arXiv:1607.0200
Constraint checking during error recovery
The system-level software onboard a spacecraft is responsible for recovery from communication, power, thermal, and computer-health anomalies that may occur. The recovery must occur without disrupting any critical scientific or engineering activity that is executing at the time of the error. Thus, the error-recovery software may have to execute concurrently with the ongoing acquisition of scientific data or with spacecraft maneuvers. This work provides a technique by which the rules that constrain the concurrent execution of these processes can be modeled in a graph. An algorithm is described that uses this model to validate that the constraints hold for all concurrent executions of the error-recovery software with the software that controls the science and engineering activities of the spacecraft. The results are applicable to a variety of control systems with critical constraints on the timing and ordering of the events they control
SHOP2: An HTN Planning System
The SHOP2 planning system received one of the awards for distinguished
performance in the 2002 International Planning Competition. This paper
describes the features of SHOP2 which enabled it to excel in the competition,
especially those aspects of SHOP2 that deal with temporal and metric planning
domains
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