7,105 research outputs found
Stochastic simulation efficiency
The work described in this report can be broadly divided into two sections. The first section considers two export features. We describe how the export for stochastic Petri nets to SBML level 1 has been added to the Petri net modelling and simulation tool Snoopy. This task was accomplished by making appropriate changes to the existing export code to generate SBML level 2. Also we demonstrate in detail, how the direct export for coloured Petri nets to both levels (i.e. 1 and 2) of SBML was realised. The next section summarises the performed comparison of different stochastic simulation tools for biochemical reaction networks. We first compare BioNetGen and SSC with each other by performing simulations on non-coloured Petri nets. Then, we compare the remaining four tools, i.e. Cain, Marcie, Snoopy and Stochkit with each other by performing simulation on coloured Petri nets.
This work builds on results by Aman Sinha [19]
Уравнения состояний стохастических временных сетей Петри с информационными связями
Розглянуто застосування мереж Петрі з часовими затримками для імітаційного моделювання систем. Отримано рівняння перетворень стану мережі Петрі та фундаментальні матричні рівняння стохастичної мережі Петрі з часовими затримками, багатоканальними та конфліктними переходами, інформаційними зв’язками.The use of timed Petri nets in systems simulation is analyzed. The equations of timed Petri net state transformations and fundamental matrix equations of stochastic timed Petri net with conflict and multi-transitions, with information ties are obtained
PETRI NET BASED APPROACHES TO MANUFACTURING SYSTEMS
This paper describes the planning in manufacturing systems. The skeleton and the functionality of a Petri Net Toolbox, embedded in the Matlab environment, are briefly presented, as offering a collection of instruments devoted to simulation, analysis and synthesis of discrete event systems. Timed Petri Nets are used to model operational and routing in production systems. A generalized multi productive machine modules is defined, adapter to system feature, repeated and connected to compose the TPN models of production systems with different levels of routing and operation. The present paper approaches the stochastic medium considered to be fundamental in describing the changes and the aleatory variations during the desertion process of machines and blocking times in the processing activity. We intend to present a simulated model according to which we can establish the time variation and the outputs process in a simple production system.Petri Nets, discrete event, manufacturing systems
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
Analysis of signalling pathways using the prism model checker
We describe a new modelling and analysis approach for signal
transduction networks in the presence of incomplete data. We illustrate
the approach with an example, the RKIP inhibited ERK pathway
[1]. Our models are based on high level descriptions of continuous time
Markov chains: reactions are modelled as synchronous processes and concentrations
are modelled by discrete, abstract quantities. The main advantage
of our approach is that using a (continuous time) stochastic logic
and the PRISM model checker, we can perform quantitative analysis of
queries such as if a concentration reaches a certain level, will it remain at
that level thereafter? We also perform standard simulations and compare
our results with a traditional ordinary differential equation model. An
interesting result is that for the example pathway, only a small number
of discrete data values is required to render the simulations practically
indistinguishable
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
Dependability Analysis of Control Systems using SystemC and Statistical Model Checking
Stochastic Petri nets are commonly used for modeling distributed systems in
order to study their performance and dependability. This paper proposes a
realization of stochastic Petri nets in SystemC for modeling large embedded
control systems. Then statistical model checking is used to analyze the
dependability of the constructed model. Our verification framework allows users
to express a wide range of useful properties to be verified which is
illustrated through a case study
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
Abridged Petri Nets
A new graphical framework, Abridged Petri Nets (APNs) is introduced for
bottom-up modeling of complex stochastic systems. APNs are similar to
Stochastic Petri Nets (SPNs) in as much as they both rely on component-based
representation of system state space, in contrast to Markov chains that
explicitly model the states of an entire system. In both frameworks, so-called
tokens (denoted as small circles) represent individual entities comprising the
system; however, SPN graphs contain two distinct types of nodes (called places
and transitions) with transitions serving the purpose of routing tokens among
places. As a result, a pair of place nodes in SPNs can be linked to each other
only via a transient stop, a transition node. In contrast, APN graphs link
place nodes directly by arcs (transitions), similar to state space diagrams for
Markov chains, and separate transition nodes are not needed.
Tokens in APN are distinct and have labels that can assume both discrete
values ("colors") and continuous values ("ages"), both of which can change
during simulation. Component interactions are modeled in APNs using triggers,
which are either inhibitors or enablers (the inhibitors' opposites).
Hierarchical construction of APNs rely on using stacks (layers) of submodels
with automatically matching color policies. As a result, APNs provide at least
the same modeling power as SPNs, but, as demonstrated by means of several
examples, the resulting models are often more compact and transparent,
therefore facilitating more efficient performance evaluation of complex
systems.Comment: 17 figure
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