7,546 research outputs found
Synthesis and Analysis of Product-form Petri Nets
For a large Markovian model, a "product form" is an explicit description of
the steady-state behaviour which is otherwise generally untractable. Being
first introduced in queueing networks, it has been adapted to Markovian Petri
nets. Here we address three relevant issues for product-form Petri nets which
were left fully or partially open: (1) we provide a sound and complete set of
rules for the synthesis; (2) we characterise the exact complexity of classical
problems like reachability; (3) we introduce a new subclass for which the
normalising constant (a crucial value for product-form expression) can be
efficiently computed.Comment: This is a version including proofs of the conference paper: Haddad,
Mairesse and Nguyen. Synthesis and Analysis of Product-form Petri Nets.
Accepted at the conference Petri Nets 201
Modelling epistasis in genetic disease using Petri nets, evolutionary computation and frequent itemset mining
Petri nets are useful for mathematically modelling disease-causing genetic epistasis. A Petri net model of an interaction has the potential to lead to biological insight into the cause of a genetic disease. However, defining a Petri net by hand for a particular interaction is extremely difficult because of the sheer complexity of the problem and degrees of freedom inherent in a Petri netâs architecture.
We propose therefore a novel method, based on evolutionary computation and data mining, for automatically constructing Petri net models of non-linear gene interactions. The method comprises two main steps. Firstly, an initial partial Petri net is set up with several repeated sub-nets that model individual genes and a set of constraints, comprising relevant common sense and biological knowledge, is also defined. These constraints characterise the class of Petri nets that are desired. Secondly, this initial Petri net structure and the constraints are used as the input to a genetic algorithm. The genetic algorithm searches for a Petri net architecture that is both a superset of the initial net, and also conforms to all of the given constraints. The genetic algorithm evaluation function that we employ gives equal weighting to both the accuracy of the net and also its parsimony.
We demonstrate our method using an epistatic model related to the presence of digital ulcers in systemic sclerosis patients that was recently reported in the literature. Our results show that although individual âperfectâ Petri nets can frequently be discovered for this interaction, the true value of this approach lies in generating many different perfect nets, and applying data mining techniques to them in order to elucidate common and statistically significant patterns of interaction
A case study in model-driven synthetic biology
We report on a case study in synthetic biology, demonstrating the modeldriven
design of a self-powering electrochemical biosensor. An essential result of
the design process is a general template of a biosensor, which can be instantiated
to be adapted to specific pollutants. This template represents a gene expression network
extended by metabolic activity. We illustrate the model-based analysis of this
template using qualitative, stochastic and continuous Petri nets and related analysis
techniques, contributing to a reliable and robust design
A review of information flow diagrammatic models for product-service systems
A product-service system (PSS) is a combination of products and services to
create value for both customers and manufacturers. Modelling a PSS based on
function orientation offers a useful way to distinguish system inputs and
outputs with regards to how data are consumed and information is used, i.e.
information flow. This article presents a review of diagrammatic information
flow tools, which are designed to describe a system through its functions. The
origin, concept and applications of these tools are investigated, followed by an
analysis of information flow modelling with regards to key PSS properties. A
case study of selection laser melting technology implemented as PSS will then be
used to show the application of information flow modelling for PSS design. A
discussion based on the usefulness of the tools in modelling the key elements of
PSS and possible future research directions are also presented
Computational Modeling for the Activation Cycle of G-proteins by G-protein-coupled Receptors
In this paper, we survey five different computational modeling methods. For
comparison, we use the activation cycle of G-proteins that regulate cellular
signaling events downstream of G-protein-coupled receptors (GPCRs) as a driving
example. Starting from an existing Ordinary Differential Equations (ODEs)
model, we implement the G-protein cycle in the stochastic Pi-calculus using
SPiM, as Petri-nets using Cell Illustrator, in the Kappa Language using
Cellucidate, and in Bio-PEPA using the Bio-PEPA eclipse plug in. We also
provide a high-level notation to abstract away from communication primitives
that may be unfamiliar to the average biologist, and we show how to translate
high-level programs into stochastic Pi-calculus processes and chemical
reactions.Comment: In Proceedings MeCBIC 2010, arXiv:1011.005
A bibliography on formal methods for system specification, design and validation
Literature on the specification, design, verification, testing, and evaluation of avionics systems was surveyed, providing 655 citations. Journal papers, conference papers, and technical reports are included. Manual and computer-based methods were employed. Keywords used in the online search are listed
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