Integrative biological systems modeling: challenges and opportunities

Most biological systems are by nature hybrids consist of interacting discrete and continuous components, which may even operate on different time scales. Therefore, it is desirable to establish modeling frameworks that are capable of combining deterministic and stochastic, discrete and continuous, as well as multi-timescale features. In the context of molecular systems biology, an example for the need of such a combination is the investigation of integrated biological pathways that contain gene regulatory, metabolic and signaling components, which may operate on different time scales and involve on-off switches as well as stochastic effects. The implementation of integrated hybrid systems is not trivial because most software is limited to one or the other of the dichotomies above. In this study, we first review the motivation for hybrid modeling. Secondly, by using the example of a toggle switch model, we illustrate a recently developed modeling framework that is based on the combination of biochemical systems theory (BST) and hybrid functional Petri nets (HFPN). Finally, we discuss remaining challenges and future opportunities.     

基于Petri网的数字系统建模和VHDL实现

基于Petri网的数字系统的建模及其硬件实现方法已经得到了广泛的研究,然而现有的方法主要适用于同步电路,由此提出了一种基于Petri网的数字系统建模和VHDL实现的新方法。首先定义了一种广义同步自控网系统,解决了数字系统的Petri网建模问题。基于一种带优先级的多输入多时钟D触发器,设计了对应的软IP核,进而探讨了广义同步自控网系统模型到VHDL代码的具体转换方法。设计的CAD工具支持数字系统的建模、功能分析与代码转换功能。通过设计示例表明了所述方法和相关工具的有效性。     

A modeling strategy for hybrid systems based on event structures

This paper considers hybrid systems which are continuous/discrete-time systems interacting with a decision maker which oversees the control and structure of the continuous/discrete-time system. These two segments combine with a processor which evaluates data to produce a three-segment model of a hybrid system having sufficient flexibility to represent a broad range of real-time situations and sufficient generality to incorporate the essential aspects of other models into a single framework. In particular the paper uses a graphically expressive controlled Petri net formulation of the decision maker and any of the usual models for the continuous/discrete-time system. Interaction between the systems occurs via three types of events: continuous/discrete-time events, decision-making events, and processor events. These types of events and their composition are rigorously defined to produce event structures and event histories. These events and event histories are used for the domain of interaction functions which specify the channels of communication between the three essential segments of the hybrid system. The event-based domains allow the disassociation of these communication channels from dependence on particular kinds of models or applications. The range of the interaction functions are binary vector-valued indicating the activation/deactivation processes in the respective segments. The entire modeling strategy is motivated by applications and models found in the literature especially flexible manufacturing systems and the C-net model of a hybrid system.This work was partially supported by the National Science Foundation under Grant No. ECS-8800910.     

考虑环境因素的分布式系统可靠性建模及其分析

为建立可变工作环境下分布式系统可靠性模型,提出受控混合随机Petri网,即用连续库所中的托肯控制离散变迁的变迁率．以此反映工作环境对部件可靠性的影响,从而推理出环境对系统可靠性的影响．在此模型的基础上,采用蒙特卡罗方法进行不同环境下系统可靠性仿真求解,解决了可变工作环境下分布式系统的可靠性建模及其分析问题．最后,以一个C^4ISR系统为例说明了该方法是一种考虑可变工作环境影响的分布式系统可靠性分析的可行方法．     

Comparison of Hybrid Systems and Fluid Stochastic Petri Nets

Hybrid Systems are modelsof interacting digital and continuous devices with applicationsin the control of aircraft, computers, or modern cars for instance.Concurrently, Fluid Stochastic Petri Nets (FSPNs) have been introducedas an extension of stochastic Petri nets to model physical systemsthat contain continuous fluid quantities controlled by discretelogic, as well as a means to deal with the possible state explosionof discrete models. Of course, an FSPN is by definition a hybridsystem but in this paper, we compare a general hybrid systemsformalism with FSPN formalism. The conclusion of this paper,suplemented by some examples, is that fluid stochastic Petrinets and hybrid system formalism can be converted from one tothe other. Although there is a price to pay for such a conversion,the conversion can transfer the solution methods from one tothe other and thus help the development of both formalisms.     

GemCell: A generic platform for modeling multi-cellular biological systems

The mass and complexity of biological information requires computer-aided simulation and analysis to help scientists achieve understanding and guide experimentation. Although living organisms are composed of cells, actual genomic and proteomic data have not yet led to a satisfactory model of working cell in silico. We have set out to devise a user-friendly generic platform, GemCell, for Generic Executable Modeling of Cells, based on whole, functioning cells. Starting with the cell simplifies life, because all cells expresses essentially five generic types of behavior: replication, death, movement (including change of shape and adherence), export (secretion, signaling, etc.) and import (receiving signals, metabolites, phagocytosis, etc.). The details of these behaviors are specified in GemCell for particular kinds of cells as part of a database of biological specifics (the DBS), which specifies the cell properties and functions that depend on the cell’s history, state, environment, etc. The DBS is designed in an intuitive fashion, so users are able to easily insert their data of interest. The generic part of GemCell, built using Statecharts, is a fully dynamic model of a cell, its interactions with the environment and its resulting behavior, individually and collectively. Model specificity emerges from the DBS, so that model execution is carried out by the statecharts executing with the aid of specific data extracted from the DBS dynamically. Our long term goal is for GemCell to serve as a broadly applicable platform for biological modeling and analysis, supporting user-friendly in silico experimentation, animation, discovery of emergent properties, and hypothesis testing, for a wide variety of biological systems.     

基于CPN的物流配送系统模型正确性的证明

利用分层有色Petri网建立物流配送模型,一方面减少了建立模型的复杂性,另一方面为模型正确性的证明提供了数据支持。对所建模型进行仿真获得的数据,可以从四个方面确保模型的正确性。使用分层有色Petri网进行层次化设计不仅可以增加模型的直观性而且降低了模型的复杂性,在确保模型正确性的同时也为物流仿真软件体系结构的模块化建立了良好的基础。     

Process vs resource‐oriented Petri net modeling of automated manufacturing systems

Since the 1980s, Petri nets (PN) have been widely used to model automated manufacturing systems (AMS) for analysis, performance evaluation, simulation, and control. They are mostly based on process‐oriented modeling methods and thus termed as process‐oriented PN (POPN) in this paper. The recent study of deadlock avoidance problems in AMS led to another type of PN called resource‐oriented PN (ROPN). This paper, for the first time, compares these two modeling methods and resultant models in terms of modeling power, model complexity for analysis and control, and some critical properties. POPN models the part production processes straightforwardly, while ROPN is more compact and effective for deadlock resolution. The relations between these two models are investigated. Several examples are used to illustrate them. Copyright © 2010 John Wiley and Sons Asia Pte Ltd and Chinese Automatic Control Society     

基于等级PRES+的嵌入式系统的建模与实现

为了有效的描绘规模较大的系统,需要一个分层机制,使模型可以有条理地构建.它由简单的单元组件构成,使得设计师在每个描述级上都可以很容易理解.提出并定义了用于形式化描述嵌入式系统建模的petri网的分层概念,显示了一个规模较大系统中的小部件如何使用层次的概念进行转换.该方法使得复杂的嵌入式系统描述更加模块化,具有可重用性,提高了嵌入式系统建模和分析的效率.通过一个实例表明了该方法的可行性.     

生化网络的随机Petri网建模与分析

细胞的行为是随机性的,学习细胞中的随机性有助于理解细胞的组织,设计和进化。建立、确认和分析随机的生化网络模型是当前计算系统生物学领域的一个重要研究主题。当前,标准的Petri网模型已经成为生化网络模拟和定性分析的有力工具。尝试使用随机Petri网对生化网络进行建模与分析,简单描述了随机Petri网理论对标准Petri网的扩充,通过对二聚作用和肌动蛋白这两个典型例子的建模与演化模拟,介绍、论证了随机Petri网理论的新应用。     

Blockchain-based recommender systems: Applications,challenges and future opportunities

Recommender systems have been widely used in different application domains including energy-preservation, e-commerce, healthcare, social media, etc. Such applications require the analysis and mining of massive amounts of various types of user data, including demographics, preferences, social interactions, etc. in order to develop accurate and precise recommender systems. Such datasets often include sensitive information, yet most recommender systems are focusing on the models’ accuracy and ignore issues related to security and the users’ privacy. Despite the efforts to overcome these problems using different risk reduction techniques, none of them has been completely successful in ensuring cryptographic security and protection of the users’ private information. To bridge this gap, the blockchain technology is presented as a promising strategy to promote security and privacy preservation in recommender systems, not only because of its security and privacy salient features, but also due to its resilience, adaptability, fault tolerance and trust characteristics. This paper presents a holistic review of blockchain-based recommender systems covering challenges, open issues and solutions. Accordingly, a well-designed taxonomy is introduced to describe the security and privacy challenges, overview existing frameworks and discuss their applications and benefits when using blockchain before indicating opportunities for future research.     

并行计算的Petri网建模和FPGA实现

在分析现有Petri网建模及其FPGA实现方法的基础上, 首先探讨了并行计算的Petri网建模方法, 将并行计算任务分解成多个并行处理单元, 用IOPT网为系统进行建模; 然后提出了构造监控层和算法层的双层结构以实现模型到FPGA实现的具体映射, 有效解决了Petri网模型中变迁只能表示简单加减运算的问题。通过矩阵乘法的应用示例, 表明了上述方法的正确性和通用性。最后提出了进一步的研究方向。     

Flexible coordinator design for modeling resource sharing in multi-agent systems

One approach to modeling multi-agent systems (MASs) is to employ a method that defines components which describe the local behavior of individual agents, as well as a special component, called a coordinator. The coordinator component coordinates the resource sharing behavior among the agents. The agent models define a set of local plans, and the combination of local plans and a coordinator defines a system’s global plan. Although earlier work has provided the base functionality needed to synthesize inter-agent resource sharing behavior for a global, conflict-free MAS environment, the lack of coordination flexibility limits the modeling capability at both the local plan level and the global plan level. In this paper, we describe a flexible design method that supports a range of coordinator components. The method defines four levels of coordination and an associated four-step coordinator generation process, which allows for the design of coordinators with increasing capabilities for handling complexity associated with resource coordination. Colored Petri net based simulation is used to analyze various properties that derive from different coordinators and synthesis of a reduced coordinator component is discussed for cases that involve homogeneous agents.     

基于随机着色Petri网的RUDP协议建模与分析

鉴于传输层传输协议TCP的低效率和UDP的不可靠性,本文提出一种新型的多帧无线传输RUDP协议,同时引入广义随机着色Petri网（GSCPN）,并利用GSCPN对本RUDP进行建模和分析,为以后更好地研究RUDP协议提供模型参考,具有很好的理论价值。     

联锁软件的统一建模语言和Petri网建模

使用统一建模语言(unified modeling language,UML)为联锁软件建立平台无关的模型(platform independent model．PIM),可以实现在异种平台间的移植和复用,并有助于自动生成测试案例和测试脚本。UML建模包括静态结构分析和动态行为分析。Petri网可对联锁软件与安全性相关的动态行为精确和严格地进行形式化描述。     

Modeling discrete event systems with state-dependent deterministic service times

In this paper extensions to the numerical solution method of deterministic and stochastic Petri nets (DSPNs) are introduced in order to cope with deterministic transitions with marking-dependent firing delays. The basic idea lies in scaling each row of the generator matrix of the Markov chain subordinated to a deterministic transition with marking-dependent firing delay by the delay value corresponding to this marking. Computational formulas of this solution method are implemented in the software package DSPNexpress which completely automates the solution process of DSPNs. The extended modeling power of DSPNs is illustrated by a single-server queuing system with Poisson arrivals, degradable deterministic service requirements, and finite capacity. Christoph Lindemann was supported by the Federal Ministry for Research and Technology of Germany (BMFT) and by the German Research Council (DFG) under grants ITR9003 and Ho 1257/2-1, respectively. Reinhard German was supported by Siemens Corporate Research and Development and by a doctoral fellowship from the German Research Council (DFG) under grant Ho 1257/1-2.     

User modeling in dialog systems: Potentials and hazards

In order to be capable of exhibiting a wide range of cooperative behavior, a computer-based dialog system must have available assumptions about the current user's goals, plans, background knowledge and (false) beliefs, i.e., maintain a so-called user model. Apart from cooperativity aspects, such a model is also necessary for intelligent coherent dialog behavior in general. This article surveys recent research on the problem of how such a model can be constructed, represented and used by a system during its interaction with the user. Possible applications, as well as potential problems concerning the advisability of application, are then discussed. Finally, a number of guidelines are presented which should be observed in future research to reduce the risk of a potential misuse of user modeling technology.     

Petri net based decision system modeling in real-time scheduling and control of flexible automotive manufacturing systems

This paper presents the design and the implementation of a Petri net (PN) model for the control of a flexible manufacturing system (FMS). A flexible automotive manufacturing system used in this environment enables quick cell configuration, and the efficient operation of cells. In this paper, we attempt to propose a flexible automotive manufacturing approach for modeling and analysis of shop floor scheduling problem of FMSs using high-level PNs. Since PNs have emerged as the principal performance modeling tools for FMS, this paper provides an object-oriented Petri nets (OOPNs) approach to performance modeling and to implement efficient production control. In this study, we modeled the system as a timed marked graph (TMG), a well-known subclass of PNs, and we showed that the problem of performance evaluation can be reduced to a simple linear programming (LP) problem with m − n + 1 variables and n constraints, where m and n represent the number of places and transitions in the marked graph, respectively. The presented PN based method is illustrated by modeling a real-time scheduling and control for flexible automotive manufacturing system (FAMS) in Valeo Turkey.     

混杂系统的研究进展

混杂系统理论和应用是近年来的一个研究热点．在介绍混杂系统概念的基础上，对混杂系统研究中的常用模型进行分类比较，并对混杂系统的性质分析和混杂控制设计中的主要内容和主要研究方法进行总结，最后对今后的研究方向做了总体展望。