Constructing biological pathway models with hybrid functional petri nets.

PubMed

Doi, Atsushi; Fujita, Sachie; Matsuno, Hiroshi; Nagasaki, Masao; Miyano, Satoru

2011-01-01

In many research projects on modeling and analyzing biological pathways, the Petri net has been recognized as a promising method for representing biological pathways. From the pioneering works by Reddy et al., 1993, and Hofestädt, 1994, that model metabolic pathways by traditional Petri net, several enhanced Petri nets such as colored Petri net, stochastic Petri net, and hybrid Petri net have been used for modeling biological phenomena. Recently, Matsuno et al., 2003b, introduced the hybrid functional Petri net (HFPN) in order to give a more intuitive and natural modeling method for biological pathways than these existing Petri nets. Although the paper demonstrates the effectiveness of HFPN with two examples of gene regulation mechanism for circadian rhythms and apoptosis signaling pathway, there has been no detailed explanation about the method of HFPN construction for these examples. The purpose of this paper is to describe method to construct biological pathways with the HFPN step-by-step. The method is demonstrated by the well-known glycolytic pathway controlled by the lac operon gene regulatory mechanism.

Petri net modelling of biological networks.

PubMed

Chaouiya, Claudine

2007-07-01

Mathematical modelling is increasingly used to get insights into the functioning of complex biological networks. In this context, Petri nets (PNs) have recently emerged as a promising tool among the various methods employed for the modelling and analysis of molecular networks. PNs come with a series of extensions, which allow different abstraction levels, from purely qualitative to more complex quantitative models. Noteworthily, each of these models preserves the underlying graph, which depicts the interactions between the biological components. This article intends to present the basics of the approach and to foster the potential role PNs could play in the development of the computational systems biology.

TokenPasser: A petri net specification tool. Thesis

NASA Technical Reports Server (NTRS)

Mittmann, Michael

1991-01-01

In computer program design it is essential to know the effectiveness of different design options in improving performance, and dependability. This paper provides a description of a CAD tool for distributed hierarchical Petri nets. After a brief review of Petri nets, Petri net languages, and Petri net transducers, and descriptions of several current Petri net tools, the specifications and design of the TokenPasser tool are presented. TokenPasser is a tool to allow design of distributed hierarchical systems based on Petri nets. A case study for an intelligent robotic system is conducted, a coordination structure with one dispatcher controlling three coordinators is built to model a proposed robotic assembly system. The system is implemented using TokenPasser, and the results are analyzed to allow judgment of the tool.

Utilization Elementary Siphons of Petri Net to Solved Deadlocks in Flexible Manufacturing Systems

NASA Astrophysics Data System (ADS)

Abdul-Hussin, Mowafak Hassan

2015-07-01

This article presents an approach to the constructing a class structural analysis of Petri nets, where elementary siphons are mainly used in the development of a deadlock control policy of flexible manufacturing systems (FMSs), that has been exploited successfully for the design of supervisors of some supervisory control problems. Deadlock-free operation of FMSs is significant objectives of siphons in the Petri net. The structure analysis of Petri net models has efficiency in control of FMSs, however different policy can be implemented for the deadlock prevention. Petri nets models based deadlock prevention for FMS's has gained considerable interest in the development of control theory and methods for design, controlling, operation, and performance evaluation depending of the special class of Petri nets called S3PR. Both structural analysis and reachability tree analysis is used for the purposes analysis, simulation and control of Petri nets. In our ex-perimental approach based to siphon is able to resolve the problem of deadlock occurred to Petri nets that are illustrated with an FMS.

A Petri Net Approach Based Elementary Siphons Supervisor for Flexible Manufacturing Systems

NASA Astrophysics Data System (ADS)

Abdul-Hussin, Mowafak Hassan

2015-05-01

This paper presents an approach to constructing a class of an S3PR net for modeling, simulation and control of processes occurring in the flexible manufacturing system (FMS) used based elementary siphons of a Petri net. Siphons are very important to the analysis and control of deadlocks of FMS that is significant objectives of siphons. Petri net models in the efficiency structure analysis, and utilization of the FMSs when different policy can be implemented lead to the deadlock prevention. We are representing an effective deadlock-free policy of a special class of Petri nets called S3PR. Simulation of Petri net structural analysis and reachability graph analysis is used for analysis and control of Petri nets. Petri nets contain been successfully as one of the most powerful tools for modelling of FMS, where Using structural analysis, we show that liveness of such systems can be attributed to the absence of under marked siphons.

Modularization of biochemical networks based on classification of Petri net t-invariants.

PubMed

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-02-08

Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior.With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis.

Modularization of biochemical networks based on classification of Petri net t-invariants

PubMed Central

Grafahrend-Belau, Eva; Schreiber, Falk; Heiner, Monika; Sackmann, Andrea; Junker, Björn H; Grunwald, Stefanie; Speer, Astrid; Winder, Katja; Koch, Ina

2008-01-01

Background Structural analysis of biochemical networks is a growing field in bioinformatics and systems biology. The availability of an increasing amount of biological data from molecular biological networks promises a deeper understanding but confronts researchers with the problem of combinatorial explosion. The amount of qualitative network data is growing much faster than the amount of quantitative data, such as enzyme kinetics. In many cases it is even impossible to measure quantitative data because of limitations of experimental methods, or for ethical reasons. Thus, a huge amount of qualitative data, such as interaction data, is available, but it was not sufficiently used for modeling purposes, until now. New approaches have been developed, but the complexity of data often limits the application of many of the methods. Biochemical Petri nets make it possible to explore static and dynamic qualitative system properties. One Petri net approach is model validation based on the computation of the system's invariant properties, focusing on t-invariants. T-invariants correspond to subnetworks, which describe the basic system behavior. With increasing system complexity, the basic behavior can only be expressed by a huge number of t-invariants. According to our validation criteria for biochemical Petri nets, the necessary verification of the biological meaning, by interpreting each subnetwork (t-invariant) manually, is not possible anymore. Thus, an automated, biologically meaningful classification would be helpful in analyzing t-invariants, and supporting the understanding of the basic behavior of the considered biological system. Methods Here, we introduce a new approach to automatically classify t-invariants to cope with network complexity. We apply clustering techniques such as UPGMA, Complete Linkage, Single Linkage, and Neighbor Joining in combination with different distance measures to get biologically meaningful clusters (t-clusters), which can be interpreted as modules. To find the optimal number of t-clusters to consider for interpretation, the cluster validity measure, Silhouette Width, is applied. Results We considered two different case studies as examples: a small signal transduction pathway (pheromone response pathway in Saccharomyces cerevisiae) and a medium-sized gene regulatory network (gene regulation of Duchenne muscular dystrophy). We automatically classified the t-invariants into functionally distinct t-clusters, which could be interpreted biologically as functional modules in the network. We found differences in the suitability of the various distance measures as well as the clustering methods. In terms of a biologically meaningful classification of t-invariants, the best results are obtained using the Tanimoto distance measure. Considering clustering methods, the obtained results suggest that UPGMA and Complete Linkage are suitable for clustering t-invariants with respect to the biological interpretability. Conclusion We propose a new approach for the biological classification of Petri net t-invariants based on cluster analysis. Due to the biologically meaningful data reduction and structuring of network processes, large sets of t-invariants can be evaluated, allowing for model validation of qualitative biochemical Petri nets. This approach can also be applied to elementary mode analysis. PMID:18257938

Topological analysis of metabolic networks based on petri net theory.

PubMed

Zevedei-Oancea, Ionela; Schuster, Stefan

2011-01-01

Petri net concepts provide additional tools for the modelling of metabolic networks. Here, the similarities between the counterparts in traditional biochemical modelling and Petri net theory are discussed. For example the stoichiometry matrix of a metabolic network corresponds to the incidence matrix of the Petri net. The flux modes and conservation relations have the T-invariants, respectively, P-invariants as counterparts. We reveal the biological meaning of some notions specific to the Petri net framework (traps, siphons, deadlocks, liveness). We focus on the topological analysis rather than on the analysis of the dynamic behaviour. The treatment of external metabolites is discussed. Some simple theoretical examples are presented for illustration. Also the Petri nets corresponding to some biochemical networks are built to support our results. For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps. All Petri net properties treated in this contribution are exemplified on a system extracted from nucleotide metabolism.

Topological analysis of metabolic networks based on Petri net theory.

PubMed

Zevedei-Oancea, Ionela; Schuster, Stefan

2003-01-01

Petri net concepts provide additional tools for the modelling of metabolic networks. Here, the similarities between the counterparts in traditional biochemical modelling and Petri net theory are discussed. For example the stoichiometry matrix of a metabolic network corresponds to the incidence matrix of the Petri net. The flux modes and conservation relations have the T-invariants, respectively, P-invariants as counterparts. We reveal the biological meaning of some notions specific to the Petri net framework (traps, siphons, deadlocks, liveness). We focus on the topological analysis rather than on the analysis of the dynamic behaviour. The treatment of external metabolites is discussed. Some simple theoretical examples are presented for illustration. Also the Petri nets corresponding to some biochemical networks are built to support our results. For example, the role of triose phosphate isomerase (TPI) in Trypanosoma brucei metabolism is evaluated by detecting siphons and traps. All Petri net properties treated in this contribution are exemplified on a system extracted from nucleotide metabolism.

Bi-directional transition nets

NASA Astrophysics Data System (ADS)

Staines, Anthony Spiteri

2017-06-01

Ordinary Petri nets are forward directed transition systems. Modern transition systems events and event flows are reversible. Hence modeling structures that reflect this are important. The creation of a bi-directional Petri net extends the modeling power of Petri nets. This work presents the successful implementation of a bi-directional transition net. Some toy examples in comparison to Petri nets are given showing the increased modeling power in a compacted form. The results show some interesting findings on how the expressive power of these structures has been increased.

Ontology based standardization of Petri net modeling for signaling pathways.

PubMed

Takai-Igarashi, Takako

2005-01-01

Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Ontology based standardization of petri net modeling for signaling pathways.

PubMed

Takai-Igarashi, Takako

2011-01-01

Taking account of the great availability of Petri nets in modeling and analyzing large complicated signaling networks, semantics of Petri nets is in need of systematization for the purpose of consistency and reusability of the models. This paper reports on standardization of units of Petri nets on the basis of an ontology that gives an intrinsic definition to the process of signaling in signaling pathways.

Modeling of Electrocardiograph Telediagnosing System Based on Petri Net

NASA Astrophysics Data System (ADS)

Hu, Wensong; Li, Ming; Li, Lan

This paper analyzed the characteristics of the electrocardiograph telediagnosing system. Firstly, we introduce the system and Petri nets. Secondly, we built a topological diagram of this system. Then we use Petri nets to show the physical process of this system. Finally, we verified the model of the electrocardiograph telediagnosing system. With the help of model based on Petri nets, we analyzed the system performance and feasibility.

Task sequence planning in a robot workcell using AND/OR nets

NASA Technical Reports Server (NTRS)

Cao, Tiehua; Sanderson, Arthur C.

1991-01-01

An approach to task sequence planning for a generalized robotic manufacturing or material handling workcell is described. Given the descriptions of the objects in this system and all feasible geometric relationships among these objects, an AND/OR net which describes the relationships of all feasible geometric states and associated feasibility criteria for net transitions is generated. This AND/OR net is mapped into a Petri net which incorporates all feasible sequences of operations. The resulting Petri net is shown to be bounded and have guaranteed properties of liveness, safeness, and reversibility. Sequences are found from the reachability tree of the Petri net. Feasibility criteria for net transitions may be used to generate an extended Petri net representation of lower level command sequences. The resulting Petri net representation may be used for on-line scheduling and control of the system of feasible sequences. A simulation example of the sequences is described.

Isomorphisms between Petri nets and dataflow graphs

NASA Technical Reports Server (NTRS)

Kavi, Krishna M.; Buckles, Billy P.; Bhat, U. Narayan

1987-01-01

Dataflow graphs are a generalized model of computation. Uninterpreted dataflow graphs with nondeterminism resolved via probabilities are shown to be isomorphic to a class of Petri nets known as free choice nets. Petri net analysis methods are readily available in the literature and this result makes those methods accessible to dataflow research. Nevertheless, combinatorial explosion can render Petri net analysis inoperative. Using a previously known technique for decomposing free choice nets into smaller components, it is demonstrated that, in principle, it is possible to determine aspects of the overall behavior from the particular behavior of components.

Quasi-Steady-State Analysis based on Structural Modules and Timed Petri Net Predict System's Dynamics: The Life Cycle of the Insulin Receptor.

PubMed

Scheidel, Jennifer; Lindauer, Klaus; Ackermann, Jörg; Koch, Ina

2015-12-17

The insulin-dependent activation and recycling of the insulin receptor play an essential role in the regulation of the energy metabolism, leading to a special interest for pharmaceutical applications. Thus, the recycling of the insulin receptor has been intensively investigated, experimentally as well as theoretically. We developed a time-resolved, discrete model to describe stochastic dynamics and study the approximation of non-linear dynamics in the context of timed Petri nets. Additionally, using a graph-theoretical approach, we analyzed the structure of the regulatory system and demonstrated the close interrelation of structural network properties with the kinetic behavior. The transition invariants decomposed the model into overlapping subnetworks of various sizes, which represent basic functional modules. Moreover, we computed the quasi-steady states of these subnetworks and demonstrated that they are fundamental to understand the dynamic behavior of the system. The Petri net approach confirms the experimental results of insulin-stimulated degradation of the insulin receptor, which represents a common feature of insulin-resistant, hyperinsulinaemic states.

Algebraic properties of automata associated to Petri nets and applications to computation in biological systems.

PubMed

Egri-Nagy, Attila; Nehaniv, Chrystopher L

2008-01-01

Biochemical and genetic regulatory networks are often modeled by Petri nets. We study the algebraic structure of the computations carried out by Petri nets from the viewpoint of algebraic automata theory. Petri nets comprise a formalized graphical modeling language, often used to describe computation occurring within biochemical and genetic regulatory networks, but the semantics may be interpreted in different ways in the realm of automata. Therefore, there are several different ways to turn a Petri net into a state-transition automaton. Here, we systematically investigate different conversion methods and describe cases where they may yield radically different algebraic structures. We focus on the existence of group components of the corresponding transformation semigroups, as these reflect symmetries of the computation occurring within the biological system under study. Results are illustrated by applications to the Petri net modelling of intermediary metabolism. Petri nets with inhibition are shown to be computationally rich, regardless of the particular interpretation method. Along these lines we provide a mathematical argument suggesting a reason for the apparent all-pervasiveness of inhibitory connections in living systems.

Scheduling multirobot operations in manufacturing by truncated Petri nets

NASA Astrophysics Data System (ADS)

Chen, Qin; Luh, J. Y.

1995-08-01

Scheduling of operational sequences in manufacturing processes is one of the important problems in automation. Methods of applying Petri nets to model and analyze the problem with constraints on precedence relations, multiple resources allocation, etc. have been available in literature. Searching for an optimum schedule can be implemented by combining the branch-and-bound technique with the execution of the timed Petri net. The process usually produces a large Petri net which is practically not manageable. This disadvantage, however, can be handled by a truncation technique which divides the original large Petri net into several smaller size subnets. The complexity involved in the analysis of each subnet individually is greatly reduced. However, when the locally optimum schedules of the resulting subnets are combined together, it may not yield an overall optimum schedule for the original Petri net. To circumvent this problem, algorithms are developed based on the concepts of Petri net execution and modified branch-and-bound process. The developed technique is applied to a multi-robot task scheduling problem of the manufacturing work cell.

Software Tool Integrating Data Flow Diagrams and Petri Nets

NASA Technical Reports Server (NTRS)

Thronesbery, Carroll; Tavana, Madjid

2010-01-01

Data Flow Diagram - Petri Net (DFPN) is a software tool for analyzing other software to be developed. The full name of this program reflects its design, which combines the benefit of data-flow diagrams (which are typically favored by software analysts) with the power and precision of Petri-net models, without requiring specialized Petri-net training. (A Petri net is a particular type of directed graph, a description of which would exceed the scope of this article.) DFPN assists a software analyst in drawing and specifying a data-flow diagram, then translates the diagram into a Petri net, then enables graphical tracing of execution paths through the Petri net for verification, by the end user, of the properties of the software to be developed. In comparison with prior means of verifying the properties of software to be developed, DFPN makes verification by the end user more nearly certain, thereby making it easier to identify and correct misconceptions earlier in the development process, when correction is less expensive. After the verification by the end user, DFPN generates a printable system specification in the form of descriptions of processes and data.

Snoopy--a unifying Petri net framework to investigate biomolecular networks.

PubMed

Rohr, Christian; Marwan, Wolfgang; Heiner, Monika

2010-04-01

To investigate biomolecular networks, Snoopy provides a unifying Petri net framework comprising a family of related Petri net classes. Models can be hierarchically structured, allowing for the mastering of larger networks. To move easily between the qualitative, stochastic and continuous modelling paradigms, models can be converted into each other. We get models sharing structure, but specialized by their kinetic information. The analysis and iterative reverse engineering of biomolecular networks is supported by the simultaneous use of several Petri net classes, while the graphical user interface adapts dynamically to the active one. Built-in animation and simulation are complemented by exports to various analysis tools. Snoopy facilitates the addition of new Petri net classes thanks to its generic design. Our tool with Petri net samples is available free of charge for non-commercial use at http://www-dssz.informatik.tu-cottbus.de/snoopy.html; supported operating systems: Mac OS X, Windows and Linux (selected distributions).

Optimal management of reconfigurable manufacturing system modeling with Petri nets developed three-dimensional - RPD3D

NASA Astrophysics Data System (ADS)

Teodor, F.; Marinescu, V.; Epureanu, A.

2016-11-01

Modeling of reconfigurable manufacturing systems would have done using existing Petri net types, but the complexity and dynamics of the new manufacturing system, mainly data reconfiguration feature, required looking for a more compact representation with many variables that to model as accurately not only the normal operation of the production system but can capture and model and reconfiguration process. Thus, it was necessary to create a new class of Petri nets, called RPD3D (Developed Petri nets with three dimensional) showing the name of both lineage (new class derived from Petri nets developed, created in 2000 by Prof. Dr. Ing Vasile Marinescu in his doctoral thesis) [1], but the most important of the new features defining (transformation from one 2D model into a 3D model).The idea was to introduce the classical model of a Petri third dimension to be able to overlay multiple levels (layers) formed in 2D or 3D Petri nets that interact with each other (receiving or giving commands to enable or disable the various modules together simulating the operation of reconfigurable manufacturing systems). The aim is to present a new type of Petri nets called RPD3D - Developed Petri three-dimensional model used for optimal control and simulation of reconfigurable manufacturing systems manufacture of products such systems.

The equivalency between logic Petri workflow nets and workflow nets.

PubMed

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented.

The Equivalency between Logic Petri Workflow Nets and Workflow Nets

PubMed Central

Wang, Jing; Yu, ShuXia; Du, YuYue

2015-01-01

Logic Petri nets (LPNs) can describe and analyze batch processing functions and passing value indeterminacy in cooperative systems. Logic Petri workflow nets (LPWNs) are proposed based on LPNs in this paper. Process mining is regarded as an important bridge between modeling and analysis of data mining and business process. Workflow nets (WF-nets) are the extension to Petri nets (PNs), and have successfully been used to process mining. Some shortcomings cannot be avoided in process mining, such as duplicate tasks, invisible tasks, and the noise of logs. The online shop in electronic commerce in this paper is modeled to prove the equivalence between LPWNs and WF-nets, and advantages of LPWNs are presented. PMID:25821845

Modeling safety requirements of an FMS using Petri-nets

NASA Astrophysics Data System (ADS)

Hanna, Moheb M.; Buck, A. A.; Smith, R.

1993-08-01

This paper is concerned with the modelling of safety requirements using Petri nets as a tool to model and simulate a Flexible Manufacturing System (FMS). The FMS cell described comprises a pick and place robot, a multi-head drilling machine together with a vision system and illustrates how the hierarchical structure of Petri nets can be used to ensure that all fail- safe requirements are satisfied; block diagrams together with fully detailed example Petri nets are given. The work demonstrates the use of cell and robot control Petro nets together with robot subnets for the x, y and z axes and associated output nets; the control and output nets are linked together with a safety net. Individual machines are linked with the control and safety nets of an FMS at cell level. The paper also illustrates how a Petri net can act as a decision maker during image inspection and identifies the unsafe conditions that can arise within an FMS.

Fault Diagnosis System of Wind Turbine Generator Based on Petri Net

NASA Astrophysics Data System (ADS)

Zhang, Han

Petri net is an important tool for discrete event dynamic systems modeling and analysis. And it has great ability to handle concurrent phenomena and non-deterministic phenomena. Currently Petri nets used in wind turbine fault diagnosis have not participated in the actual system. This article will combine the existing fuzzy Petri net algorithms; build wind turbine control system simulation based on Siemens S7-1200 PLC, while making matlab gui interface for migration of the system to different platforms.

Identification of key regulators in glycogen utilization in E. coli based on the simulations from a hybrid functional Petri net model.

PubMed

Tian, Zhongyuan; Fauré, Adrien; Mori, Hirotada; Matsuno, Hiroshi

2013-01-01

Glycogen and glucose are two sugar sources available during the lag phase of E. coli, but the mechanism that regulates their utilization is still unclear. Attempting to unveil the relationship between glucose and glycogen, we propose an integrated hybrid functional Petri net (HFPN) model including glycolysis, PTS, glycogen metabolic pathway, and their internal regulatory systems. By comparing known biological results to this model, basic necessary regulatory mechanism for utilizing glucose and glycogen were identified as a feedback circuit in which HPr and EIIAGlc play key roles. Based on this regulatory HFPN model, we discuss the process of glycogen utilization in E. coli in the context of a systematic understanding of carbohydrate metabolism.

A Petri net controller for distributed hierarchical systems. Thesis

NASA Technical Reports Server (NTRS)

Peck, Joseph E.

1991-01-01

The solutions to a wide variety of problems are often best organized as a distributed hierarchical system. These systems can be graphically and mathematically modeled through the use of Petri nets, which can easily represent synchronous, asynchronous, and concurrent operations. This thesis presents a controller implementation based on Petri nets and a design methodology for the interconnection of distributed Petri nets. Two case studies are presented in which the controller operates a physical system, the Center for Intelligent Robotic Systems for Space Exploration Dual Arm Robotic Testbed.

Fuzzy Petri nets to model vision system decisions within a flexible manufacturing system

NASA Astrophysics Data System (ADS)

Hanna, Moheb M.; Buck, A. A.; Smith, R.

1994-10-01

The paper presents a Petri net approach to modelling, monitoring and control of the behavior of an FMS cell. The FMS cell described comprises a pick and place robot, vision system, CNC-milling machine and 3 conveyors. The work illustrates how the block diagrams in a hierarchical structure can be used to describe events at different levels of abstraction. It focuses on Fuzzy Petri nets (Fuzzy logic with Petri nets) including an artificial neural network (Fuzzy Neural Petri nets) to model and control vision system decisions and robot sequences within an FMS cell. This methodology can be used as a graphical modelling tool to monitor and control the imprecise, vague and uncertain situations, and determine the quality of the output product of an FMS cell.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory.

PubMed

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality.

Automation of Presentation Record Production Based on Rich-Media Technology Using SNT Petri Nets Theory

PubMed Central

Martiník, Ivo

2015-01-01

Rich-media describes a broad range of digital interactive media that is increasingly used in the Internet and also in the support of education. Last year, a special pilot audiovisual lecture room was built as a part of the MERLINGO (MEdia-rich Repository of LearnING Objects) project solution. It contains all the elements of the modern lecture room determined for the implementation of presentation recordings based on the rich-media technologies and their publication online or on-demand featuring the access of all its elements in the automated mode including automatic editing. Property-preserving Petri net process algebras (PPPA) were designed for the specification and verification of the Petri net processes. PPPA does not need to verify the composition of the Petri net processes because all their algebraic operators preserve the specified set of the properties. These original PPPA are significantly generalized for the newly introduced class of the SNT Petri process and agent nets in this paper. The PLACE-SUBST and ASYNC-PROC algebraic operators are defined for this class of Petri nets and their chosen properties are proved. The SNT Petri process and agent nets theory were significantly applied at the design, verification, and implementation of the programming system ensuring the pilot audiovisual lecture room functionality. PMID:26258164

A versatile petri net based architecture for modeling and simulation of complex biological processes.

PubMed

Nagasaki, Masao; Doi, Atsushi; Matsuno, Hiroshi; Miyano, Satoru

2004-01-01

The research on modeling and simulation of complex biological systems is getting more important in Systems Biology. In this respect, we have developed Hybrid Function Petri net (HFPN) that was newly developed from existing Petri net because of their intuitive graphical representation and their capabilities for mathematical analyses. However, in the process of modeling metabolic, gene regulatory or signal transduction pathways with the architecture, we have realized three extensions of HFPN, (i) an entity should be extended to contain more than one value, (ii) an entity should be extended to handle other primitive types, e.g. boolean, string, (iii) an entity should be extended to handle more advanced type called object that consists of variables and methods, are necessary for modeling biological systems with Petri net based architecture. To deal with it, we define a new enhanced Petri net called hybrid functional Petri net with extension (HFPNe). To demonstrate the effectiveness of the enhancements, we model and simulate with HFPNe four biological processes that are diffcult to represent with the previous architecture HFPN.

Petri net based model of the body iron homeostasis.

PubMed

Formanowicz, Dorota; Sackmann, Andrea; Formanowicz, Piotr; Błazewicz, Jacek

2007-10-01

The body iron homeostasis is a not fully understood complex process. Despite the fact that some components of this process have been described in the literature, the complete model of the whole process has not been proposed. In this paper a Petri net based model of the body iron homeostasis is presented. Recently, Petri nets have been used for describing and analyzing various biological processes since they allow modeling the system under consideration very precisely. The main result presented in the paper is twofold, i.e., an informal description of the main part of the whole iron homeostasis process is described, and then it is also formulated in the formal language of Petri net theory. This model allows for a possible simulation of the process, since Petri net theory provides a lot of established analysis techniques.

Application of growing nested Petri nets for modeling robotic systems operating under risk

NASA Astrophysics Data System (ADS)

Sorokin, E. V.; Senkov, A. V.

2017-10-01

The paper studies the peculiarities of modeling robotic systems engaged in mining. Existing modeling mechanisms are considered, which are based on nested Petri nets, and a new formalism of growing Petri nets is presented that allows modeling robotic systems operating under risk. Modeling is provided both for the regular operation mode and for non-standard modes in which individual elements of the system can perform uncharacteristic functions. The example shows growing Petri nets that are used for modeling extraction of flat coal seams by a robotic system consisting of several different-type autonomous robots.

Quantitative petri net model of gene regulated metabolic networks in the cell.

PubMed

Chen, Ming; Hofestädt, Ralf

2011-01-01

A method to exploit hybrid Petri nets (HPN) for quantitatively modeling and simulating gene regulated metabolic networks is demonstrated. A global kinetic modeling strategy and Petri net modeling algorithm are applied to perform the bioprocess functioning and model analysis. With the model, the interrelations between pathway analysis and metabolic control mechanism are outlined. Diagrammatical results of the dynamics of metabolites are simulated and observed by implementing a HPN tool, Visual Object Net ++. An explanation of the observed behavior of the urea cycle is proposed to indicate possibilities for metabolic engineering and medical care. Finally, the perspective of Petri nets on modeling and simulation of metabolic networks is discussed.

Modeling of water treatment plant using timed continuous Petri nets

NASA Astrophysics Data System (ADS)

Nurul Fuady Adhalia, H.; Subiono, Adzkiya, Dieky

2017-08-01

Petri nets represent graphically certain conditions and rules. In this paper, we construct a model of the Water Treatment Plant (WTP) using timed continuous Petri nets. Specifically, we consider that (1) the water pump always active and (2) the water source is always available. After obtaining the model, the flow through the transitions and token conservation laws are calculated.

Petri nets SM-cover-based on heuristic coloring algorithm

NASA Astrophysics Data System (ADS)

Tkacz, Jacek; Doligalski, Michał

2015-09-01

In the paper, coloring heuristic algorithm of interpreted Petri nets is presented. Coloring is used to determine the State Machines (SM) subnets. The present algorithm reduces the Petri net in order to reduce the computational complexity and finds one of its possible State Machines cover. The proposed algorithm uses elements of interpretation of Petri nets. The obtained result may not be the best, but it is sufficient for use in rapid prototyping of logic controllers. Found SM-cover will be also used in the development of algorithms for decomposition, and modular synthesis and implementation of parallel logic controllers. Correctness developed heuristic algorithm was verified using Gentzen formal reasoning system.

A systematic petri net approach for multiple-scale modeling and simulation of biochemical processes.

PubMed

Chen, Ming; Hu, Minjie; Hofestädt, Ralf

2011-06-01

A method to exploit hybrid Petri nets for modeling and simulating biochemical processes in a systematic way was introduced. Both molecular biology and biochemical engineering aspects are manipulated. With discrete and continuous elements, the hybrid Petri nets can easily handle biochemical factors such as metabolites concentration and kinetic behaviors. It is possible to translate both molecular biological behavior and biochemical processes workflow into hybrid Petri nets in a natural manner. As an example, penicillin production bioprocess is modeled to illustrate the concepts of the methodology. Results of the dynamic of production parameters in the bioprocess were simulated and observed diagrammatically. Current problems and post-genomic perspectives were also discussed.

Modeling and performance analysis of QoS data

NASA Astrophysics Data System (ADS)

Strzeciwilk, Dariusz; Zuberek, Włodzimierz M.

2016-09-01

The article presents the results of modeling and analysis of data transmission performance on systems that support quality of service. Models are designed and tested, taking into account multiservice network architecture, i.e. supporting the transmission of data related to different classes of traffic. Studied were mechanisms of traffic shaping systems, which are based on the Priority Queuing with an integrated source of data and the various sources of data that is generated. Discussed were the basic problems of the architecture supporting QoS and queuing systems. Designed and built were models based on Petri nets, supported by temporal logics. The use of simulation tools was to verify the mechanisms of shaping traffic with the applied queuing algorithms. It is shown that temporal models of Petri nets can be effectively used in the modeling and analysis of the performance of computer networks.

An advanced environment for hybrid modeling of biological systems based on modelica.

PubMed

Pross, Sabrina; Bachmann, Bernhard

2011-01-20

Biological systems are often very complex so that an appropriate formalism is needed for modeling their behavior. Hybrid Petri Nets, consisting of time-discrete Petri Net elements as well as continuous ones, have proven to be ideal for this task. Therefore, a new Petri Net library was implemented based on the object-oriented modeling language Modelica which allows the modeling of discrete, stochastic and continuous Petri Net elements by differential, algebraic and discrete equations. An appropriate Modelica-tool performs the hybrid simulation with discrete events and the solution of continuous differential equations. A special sub-library contains so-called wrappers for specific reactions to simplify the modeling process. The Modelica-models can be connected to Simulink-models for parameter optimization, sensitivity analysis and stochastic simulation in Matlab. The present paper illustrates the implementation of the Petri Net component models, their usage within the modeling process and the coupling between the Modelica-tool Dymola and Matlab/Simulink. The application is demonstrated by modeling the metabolism of Chinese Hamster Ovary Cells.

Realization of planning design of mechanical manufacturing system by Petri net simulation model

NASA Astrophysics Data System (ADS)

Wu, Yanfang; Wan, Xin; Shi, Weixiang

1991-09-01

Planning design is to work out a more overall long-term plan. In order to guarantee a mechanical manufacturing system (MMS) designed to obtain maximum economical benefit, it is necessary to carry out a reasonable planning design for the system. First, some principles on planning design for MMS are introduced. Problems of production scheduling and their decision rules for computer simulation are presented. Realizable method of each production scheduling decision rule in Petri net model is discussed. Second, the solution of conflict rules for conflict problems during running Petri net is given. Third, based on the Petri net model of MMS which includes part flow and tool flow, according to the principle of minimum event time advance, a computer dynamic simulation of the Petri net model, that is, a computer dynamic simulation of MMS, is realized. Finally, the simulation program is applied to a simulation exmple, so the scheme of a planning design for MMS can be evaluated effectively.

A new approach for modular robot system behavioral modeling: Base on Petri net and category theory

NASA Astrophysics Data System (ADS)

Zhang, Yun; Wei, Hongxing; Yang, Bo

2018-04-01

To design modular robot system, Petri nets and category theory are combined and the ability of simulation of Petri net is discussed. According to category theory, the method of describing the category of components in the dynamic characteristics of the system is deduced. Moreover, a modular robot system is analyzed, which provides a verifiable description of the dynamic characteristics of the system.

Teaching Petri Nets Using P3

ERIC Educational Resources Information Center

Gasevic, Dragan; Devedzic, Vladan

2004-01-01

This paper presents Petri net software tool P3 that is developed for training purposes of the Architecture and organization of computers (AOC) course. The P3 has the following features: graphical modeling interface, interactive simulation by single and parallel (with previous conflict resolution) transition firing, two well-known Petri net…

An assembly process model based on object-oriented hierarchical time Petri Nets

NASA Astrophysics Data System (ADS)

Wang, Jiapeng; Liu, Shaoli; Liu, Jianhua; Du, Zenghui

2017-04-01

In order to improve the versatility, accuracy and integrity of the assembly process model of complex products, an assembly process model based on object-oriented hierarchical time Petri Nets is presented. A complete assembly process information model including assembly resources, assembly inspection, time, structure and flexible parts is established, and this model describes the static and dynamic data involved in the assembly process. Through the analysis of three-dimensional assembly process information, the assembly information is hierarchically divided from the whole, the local to the details and the subnet model of different levels of object-oriented Petri Nets is established. The communication problem between Petri subnets is solved by using message database, and it reduces the complexity of system modeling effectively. Finally, the modeling process is presented, and a five layer Petri Nets model is established based on the hoisting process of the engine compartment of a wheeled armored vehicle.

A New ’Availability-Payment’ Model for Pricing Performance-Based Logistics Contracts

DTIC Science & Technology

2014-04-30

maintenance network connected to the inventory and Original Equipment Manufacturer (OEM) used in this paper. The input to the Petri net in Figure 2 is the...contract structures. The model developed in this paper uses an affine controller to drive a discrete event simulator ( Petri net ) that produces...discrete event simulator ( Petri net ) that produces availability and cost measures. The model is used to explore the optimum availability assessment

Modeling biological gradient formation: combining partial differential equations and Petri nets.

PubMed

Bertens, Laura M F; Kleijn, Jetty; Hille, Sander C; Heiner, Monika; Koutny, Maciej; Verbeek, Fons J

2016-01-01

Both Petri nets and differential equations are important modeling tools for biological processes. In this paper we demonstrate how these two modeling techniques can be combined to describe biological gradient formation. Parameters derived from partial differential equation describing the process of gradient formation are incorporated in an abstract Petri net model. The quantitative aspects of the resulting model are validated through a case study of gradient formation in the fruit fly.

Parallel firing strategy on Petri nets: A review

NASA Astrophysics Data System (ADS)

Mavlankulov, Gairatzhan; Turaev, Sherzod; Zhumabaeva, Laula; Zhukabayeva, Tamara

2015-05-01

In this paper we review the recent results related on Petri net controlled grammars and the close related topics. Though the theme of regulated grammars is one of the classic topics in formal language theory, a Petri net controlled grammar is still interesting subject for the investigation for many reasons. This type of grammars can successfully be used in modeling new problems emerging in manufacturing systems, systems biology and other areas. Moreover, the graphically illustrability, the ability to represent both a grammar and its control in one structure, and the possibility to unify different regulated rewritings make this formalization attractive for the study. We also summarize the obtained results and propose a new conception such as parallel firing strategy on Petri Nets.

BioNetSim: a Petri net-based modeling tool for simulations of biochemical processes.

PubMed

Gao, Junhui; Li, Li; Wu, Xiaolin; Wei, Dong-Qing

2012-03-01

BioNetSim, a Petri net-based software for modeling and simulating biochemistry processes, is developed, whose design and implement are presented in this paper, including logic construction, real-time access to KEGG (Kyoto Encyclopedia of Genes and Genomes), and BioModel database. Furthermore, glycolysis is simulated as an example of its application. BioNetSim is a helpful tool for researchers to download data, model biological network, and simulate complicated biochemistry processes. Gene regulatory networks, metabolic pathways, signaling pathways, and kinetics of cell interaction are all available in BioNetSim, which makes modeling more efficient and effective. Similar to other Petri net-based softwares, BioNetSim does well in graphic application and mathematic construction. Moreover, it shows several powerful predominances. (1) It creates models in database. (2) It realizes the real-time access to KEGG and BioModel and transfers data to Petri net. (3) It provides qualitative analysis, such as computation of constants. (4) It generates graphs for tracing the concentration of every molecule during the simulation processes.

Modelling of Biometric Identification System with Given Parameters Using Colored Petri Nets

NASA Astrophysics Data System (ADS)

Petrosyan, G.; Ter-Vardanyan, L.; Gaboutchian, A.

2017-05-01

Biometric identification systems use given parameters and function on the basis of Colored Petri Nets as a modelling language developed for systems in which communication, synchronization and distributed resources play an important role. Colored Petri Nets combine the strengths of Classical Petri Nets with the power of a high-level programming language. Coloured Petri Nets have both, formal intuitive and graphical presentations. Graphical CPN model consists of a set of interacting modules which include a network of places, transitions and arcs. Mathematical representation has a well-defined syntax and semantics, as well as defines system behavioural properties. One of the best known features used in biometric is the human finger print pattern. During the last decade other human features have become of interest, such as iris-based or face recognition. The objective of this paper is to introduce the fundamental concepts of Petri Nets in relation to tooth shape analysis. Biometric identification systems functioning has two phases: data enrollment phase and identification phase. During the data enrollment phase images of teeth are added to database. This record contains enrollment data as a noisy version of the biometrical data corresponding to the individual. During the identification phase an unknown individual is observed again and is compared to the enrollment data in the database and then system estimates the individual. The purpose of modeling biometric identification system by means of Petri Nets is to reveal the following aspects of the functioning model: the efficiency of the model, behavior of the model, mistakes and accidents in the model, feasibility of the model simplification or substitution of its separate components for more effective components without interfering system functioning. The results of biometric identification system modeling and evaluating are presented and discussed.

Simulation of a Petri net-based model of the terpenoid biosynthesis pathway.

PubMed

Hawari, Aliah Hazmah; Mohamed-Hussein, Zeti-Azura

2010-02-09

The development and simulation of dynamic models of terpenoid biosynthesis has yielded a systems perspective that provides new insights into how the structure of this biochemical pathway affects compound synthesis. These insights may eventually help identify reactions that could be experimentally manipulated to amplify terpenoid production. In this study, a dynamic model of the terpenoid biosynthesis pathway was constructed based on the Hybrid Functional Petri Net (HFPN) technique. This technique is a fusion of three other extended Petri net techniques, namely Hybrid Petri Net (HPN), Dynamic Petri Net (HDN) and Functional Petri Net (FPN). The biological data needed to construct the terpenoid metabolic model were gathered from the literature and from biological databases. These data were used as building blocks to create an HFPNe model and to generate parameters that govern the global behaviour of the model. The dynamic model was simulated and validated against known experimental data obtained from extensive literature searches. The model successfully simulated metabolite concentration changes over time (pt) and the observations correlated with known data. Interactions between the intermediates that affect the production of terpenes could be observed through the introduction of inhibitors that established feedback loops within and crosstalk between the pathways. Although this metabolic model is only preliminary, it will provide a platform for analysing various high-throughput data, and it should lead to a more holistic understanding of terpenoid biosynthesis.

Multi-variants synthesis of Petri nets for FPGA devices

NASA Astrophysics Data System (ADS)

Bukowiec, Arkadiusz; Doligalski, Michał

2015-09-01

There is presented new method of synthesis of application specific logic controllers for FPGA devices. The specification of control algorithm is made with use of control interpreted Petri net (PT type). It allows specifying parallel processes in easy way. The Petri net is decomposed into state-machine type subnets. In this case, each subnet represents one parallel process. For this purpose there are applied algorithms of coloring of Petri nets. There are presented two approaches of such decomposition: with doublers of macroplaces or with one global wait place. Next, subnets are implemented into two-level logic circuit of the controller. The levels of logic circuit are obtained as a result of its architectural decomposition. The first level combinational circuit is responsible for generation of next places and second level decoder is responsible for generation output symbols. There are worked out two variants of such circuits: with one shared operational memory or with many flexible distributed memories as a decoder. Variants of Petri net decomposition and structures of logic circuits can be combined together without any restrictions. It leads to existence of four variants of multi-variants synthesis.

On determining firing delay time of transitions for Petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2010-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

Applications of the Petri net to simulate, test, and validate the performance and safety of complex, heterogeneous, multi-modality patient monitoring alarm systems.

PubMed

Sloane, E B; Gelhot, V

2004-01-01

This research is motivated by the rapid pace of medical device and information system integration. Although the ability to interconnect many medical devices and information systems may help improve patient care, there is no way to detect if incompatibilities between one or more devices might cause critical events such as patient alarms to go unnoticed or cause one or more of the devices to become stuck in a disabled state. Petri net tools allow automated testing of all possible states and transitions between devices and/or systems to detect potential failure modes in advance. This paper describes an early research project to use Petri nets to simulate and validate a multi-modality central patient monitoring system. A free Petri net tool, HPSim, is used to simulate two wireless patient monitoring networks: one with 44 heart monitors and a central monitoring system and a second version that includes an additional 44 wireless pulse oximeters. In the latter Petri net simulation, a potentially dangerous heart arrhythmia and pulse oximetry alarms were detected.

Petri net modeling of high-order genetic systems using grammatical evolution.

PubMed

Moore, Jason H; Hahn, Lance W

2003-11-01

Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two DNA sequence variations. In the present study, we evaluate whether the Petri net approach is capable of identifying biochemical networks that are consistent with disease susceptibility due to higher order nonlinear interactions between three DNA sequence variations. The results indicate that our model-building approach is capable of routinely identifying good, but not perfect, Petri net models. Ideas for improving the algorithm for this high-dimensional problem are presented.

On determining firing delay time of transitions for petri net based signaling pathways by introducing stochastic decision rules.

PubMed

Miwa, Yoshimasa; Li, Chen; Ge, Qi-Wei; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

Parameter determination is important in modeling and simulating biological pathways including signaling pathways. Parameters are determined according to biological facts obtained from biological experiments and scientific publications. However, such reliable data describing detailed reactions are not reported in most cases. This prompted us to develop a general methodology of determining the parameters of a model in the case of that no information of the underlying biological facts is provided. In this study, we use the Petri net approach for modeling signaling pathways, and propose a method to determine firing delay times of transitions for Petri net models of signaling pathways by introducing stochastic decision rules. Petri net technology provides a powerful approach to modeling and simulating various concurrent systems, and recently have been widely accepted as a description method for biological pathways. Our method enables to determine the range of firing delay time which realizes smooth token flows in the Petri net model of a signaling pathway. The availability of this method has been confirmed by the results of an application to the interleukin-1 induced signaling pathway.

Reconstructing the regulatory network controlling commitment and sporulation in Physarum polycephalum based on hierarchical Petri Net modelling and simulation.

PubMed

Marwan, Wolfgang; Sujatha, Arumugam; Starostzik, Christine

2005-10-21

We reconstruct the regulatory network controlling commitment and sporulation of Physarum polycephalum from experimental results using a hierarchical Petri Net-based modelling and simulation framework. The stochastic Petri Net consistently describes the structure and simulates the dynamics of the molecular network as analysed by genetic, biochemical and physiological experiments within a single coherent model. The Petri Net then is extended to simulate time-resolved somatic complementation experiments performed by mixing the cytoplasms of mutants altered in the sporulation response, to systematically explore the network structure and to probe its dynamics. This reverse engineering approach presumably can be employed to explore other molecular or genetic signalling systems where the activity of genes or their products can be experimentally controlled in a time-resolved manner.

Learning Petri net models of non-linear gene interactions.

PubMed

Mayo, Michael

2005-10-01

Understanding how an individual's genetic make-up influences their risk of disease is a problem of paramount importance. Although machine-learning techniques are able to uncover the relationships between genotype and disease, the problem of automatically building the best biochemical model or "explanation" of the relationship has received less attention. In this paper, I describe a method based on random hill climbing that automatically builds Petri net models of non-linear (or multi-factorial) disease-causing gene-gene interactions. Petri nets are a suitable formalism for this problem, because they are used to model concurrent, dynamic processes analogous to biochemical reaction networks. I show that this method is routinely able to identify perfect Petri net models for three disease-causing gene-gene interactions recently reported in the literature.

Application of Petri net theory for modelling and validation of the sucrose breakdown pathway in the potato tuber.

PubMed

Koch, Ina; Junker, Björn H; Heiner, Monika

2005-04-01

Because of the complexity of metabolic networks and their regulation, formal modelling is a useful method to improve the understanding of these systems. An essential step in network modelling is to validate the network model. Petri net theory provides algorithms and methods, which can be applied directly to metabolic network modelling and analysis in order to validate the model. The metabolism between sucrose and starch in the potato tuber is of great research interest. Even if the metabolism is one of the best studied in sink organs, it is not yet fully understood. We provide an approach for model validation of metabolic networks using Petri net theory, which we demonstrate for the sucrose breakdown pathway in the potato tuber. We start with hierarchical modelling of the metabolic network as a Petri net and continue with the analysis of qualitative properties of the network. The results characterize the net structure and give insights into the complex net behaviour.

Fluid Stochastic Petri Nets: Theory, Applications, and Solution

NASA Technical Reports Server (NTRS)

Horton, Graham; Kulkarni, Vidyadhar G.; Nicol, David M.; Trivedi, Kishor S.

1996-01-01

In this paper we introduce a new class of stochastic Petri nets in which one or more places can hold fluid rather than discrete tokens. We define a class of fluid stochastic Petri nets in such a way that the discrete and continuous portions may affect each other. Following this definition we provide equations for their transient and steady-state behavior. We present several examples showing the utility of the construct in communication network modeling and reliability analysis, and discuss important special cases. We then discuss numerical methods for computing the transient behavior of such nets. Finally, some numerical examples are presented.

Approximation methods for stochastic petri nets

NASA Technical Reports Server (NTRS)

Jungnitz, Hauke Joerg

1992-01-01

Stochastic Marked Graphs are a concurrent decision free formalism provided with a powerful synchronization mechanism generalizing conventional Fork Join Queueing Networks. In some particular cases the analysis of the throughput can be done analytically. Otherwise the analysis suffers from the classical state explosion problem. Embedded in the divide and conquer paradigm, approximation techniques are introduced for the analysis of stochastic marked graphs and Macroplace/Macrotransition-nets (MPMT-nets), a new subclass introduced herein. MPMT-nets are a subclass of Petri nets that allow limited choice, concurrency and sharing of resources. The modeling power of MPMT is much larger than that of marked graphs, e.g., MPMT-nets can model manufacturing flow lines with unreliable machines and dataflow graphs where choice and synchronization occur. The basic idea leads to the notion of a cut to split the original net system into two subnets. The cuts lead to two aggregated net systems where one of the subnets is reduced to a single transition. A further reduction leads to a basic skeleton. The generalization of the idea leads to multiple cuts, where single cuts can be applied recursively leading to a hierarchical decomposition. Based on the decomposition, a response time approximation technique for the performance analysis is introduced. Also, delay equivalence, which has previously been introduced in the context of marked graphs by Woodside et al., Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's method and flow equivalent aggregation are applied to the aggregated net systems. The experimental results show that response time approximation converges quickly and shows reasonable accuracy in most cases. The convergence of Marie's is slower, but the accuracy is generally better. Delay equivalence often fails to converge, while flow equivalent aggregation can lead to potentially bad results if a strong dependence of the mean completion time on the interarrival process exists.

Analysis hierarchical model for discrete event systems

NASA Astrophysics Data System (ADS)

Ciortea, E. M.

2015-11-01

The This paper presents the hierarchical model based on discrete event network for robotic systems. Based on the hierarchical approach, Petri network is analysed as a network of the highest conceptual level and the lowest level of local control. For modelling and control of complex robotic systems using extended Petri nets. Such a system is structured, controlled and analysed in this paper by using Visual Object Net ++ package that is relatively simple and easy to use, and the results are shown as representations easy to interpret. The hierarchical structure of the robotic system is implemented on computers analysed using specialized programs. Implementation of hierarchical model discrete event systems, as a real-time operating system on a computer network connected via a serial bus is possible, where each computer is dedicated to local and Petri model of a subsystem global robotic system. Since Petri models are simplified to apply general computers, analysis, modelling, complex manufacturing systems control can be achieved using Petri nets. Discrete event systems is a pragmatic tool for modelling industrial systems. For system modelling using Petri nets because we have our system where discrete event. To highlight the auxiliary time Petri model using transport stream divided into hierarchical levels and sections are analysed successively. Proposed robotic system simulation using timed Petri, offers the opportunity to view the robotic time. Application of goods or robotic and transmission times obtained by measuring spot is obtained graphics showing the average time for transport activity, using the parameters sets of finished products. individually.

Necessary and sufficient liveness condition of GS3PR Petri nets

NASA Astrophysics Data System (ADS)

Liu, GaiYun; Barkaoui, Kamel

2015-05-01

Structural analysis is one of the most important and efficient methods to investigate the behaviour of Petri nets. Liveness is a significant behavioural property of Petri nets. Siphons, as structural objects of a Petri net, are closely related to its liveness. Many deadlock control policies for flexible manufacturing systems (FMS) modelled by Petri nets are implemented via siphon control. Most of the existing methods design liveness-enforcing supervisors by adding control places for siphons based on their controllability conditions. To compute a liveness-enforcing supervisor with as much as permissive behaviour, it is both theoretically and practically significant to find an exact controllability condition for siphons. However, the existing conditions, max, max‧, and max″-controllability of siphons are all overly restrictive and generally sufficient only. This paper develops a new condition called max*-controllability of the siphons in generalised systems of simple sequential processes with resources (GS3PR), which are a net subclass that can model many real-world automated manufacturing systems. We show that a GS3PR is live if all its strict minimal siphons (SMS) are max*-controlled. Compared with the existing conditions, i.e., max-, max‧-, and max″-controllability of siphons, max*-controllability of the SMS is not only sufficient but also necessary. An example is used to illustrate the proposed method.

Modified Petri net model sensitivity to workload manipulations

NASA Technical Reports Server (NTRS)

White, S. A.; Mackinnon, D. P.; Lyman, J.

1986-01-01

Modified Petri Nets (MPNs) are investigated as a workload modeling tool. The results of an exploratory study of the sensitivity of MPNs to work load manipulations in a dual task are described. Petri nets have been used to represent systems with asynchronous, concurrent and parallel activities (Peterson, 1981). These characteristics led some researchers to suggest the use of Petri nets in workload modeling where concurrent and parallel activities are common. Petri nets are represented by places and transitions. In the workload application, places represent operator activities and transitions represent events. MPNs have been used to formally represent task events and activities of a human operator in a man-machine system. Some descriptive applications demonstrate the usefulness of MPNs in the formal representation of systems. It is the general hypothesis herein that in addition to descriptive applications, MPNs may be useful for workload estimation and prediction. The results are reported of the first of a series of experiments designed to develop and test a MPN system of workload estimation and prediction. This first experiment is a screening test of MPN model general sensitivity to changes in workload. Positive results from this experiment will justify the more complicated analyses and techniques necessary for developing a workload prediction system.

Transportation Planning with Immune System Derived Approach

NASA Astrophysics Data System (ADS)

Sugiyama, Kenji; Yaji, Yasuhito; Ootsuki, John Takuya; Fujimoto, Yasutaka; Sekiguchi, Takashi

This paper presents an immune system derived approach for planning transportation of materials between manufacturing processes in the factory. Transportation operations are modeled by Petri Net, and divided into submodels. Transportation orders are derived from the firing sequences of those submodels through convergence calculation by the immune system derived excitation and suppression operations. Basic evaluation of this approach is conducted by simulation-based investigation.

Coloured Petri Net Refinement Specification and Correctness Proof with Coq

NASA Technical Reports Server (NTRS)

Choppy, Christine; Mayero, Micaela; Petrucci, Laure

2009-01-01

In this work, we address the formalisation of symmetric nets, a subclass of coloured Petri nets, refinement in COQ. We first provide a formalisation of the net models, and of their type refinement in COQ. Then the COQ proof assistant is used to prove the refinement correctness lemma. An example adapted from a protocol example illustrates our work.

An analysis of the Petri net based model of the human body iron homeostasis process.

PubMed

Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Koch, Ina; Blazewicz, Jacek

2007-02-01

In the paper a Petri net based model of the human body iron homeostasis is presented and analyzed. The body iron homeostasis is an important but not fully understood complex process. The modeling of the process presented in the paper is expressed in the language of Petri net theory. An application of this theory to the description of biological processes allows for very precise analysis of the resulting models. Here, such an analysis of the body iron homeostasis model from a mathematical point of view is given.

An object-oriented description method of EPMM process

NASA Astrophysics Data System (ADS)

Jiang, Zuo; Yang, Fan

2017-06-01

In order to use the object-oriented mature tools and language in software process model, make the software process model more accord with the industrial standard, it’s necessary to study the object-oriented modelling of software process. Based on the formal process definition in EPMM, considering the characteristics that Petri net is mainly formal modelling tool and combining the Petri net modelling with the object-oriented modelling idea, this paper provides this implementation method to convert EPMM based on Petri net into object models based on object-oriented description.

Neural system modeling and simulation using Hybrid Functional Petri Net.

PubMed

Tang, Yin; Wang, Fei

2012-02-01

The Petri net formalism has been proved to be powerful in biological modeling. It not only boasts of a most intuitive graphical presentation but also combines the methods of classical systems biology with the discrete modeling technique. Hybrid Functional Petri Net (HFPN) was proposed specially for biological system modeling. An array of well-constructed biological models using HFPN yielded very interesting results. In this paper, we propose a method to represent neural system behavior, where biochemistry and electrical chemistry are both included using the Petri net formalism. We built a model for the adrenergic system using HFPN and employed quantitative analysis. Our simulation results match the biological data well, showing that the model is very effective. Predictions made on our model further manifest the modeling power of HFPN and improve the understanding of the adrenergic system. The file of our model and more results with their analysis are available in our supplementary material.

Holmes: a graphical tool for development, simulation and analysis of Petri net based models of complex biological systems.

PubMed

Radom, Marcin; Rybarczyk, Agnieszka; Szawulak, Bartlomiej; Andrzejewski, Hubert; Chabelski, Piotr; Kozak, Adam; Formanowicz, Piotr

2017-12-01

Model development and its analysis is a fundamental step in systems biology. The theory of Petri nets offers a tool for such a task. Since the rapid development of computer science, a variety of tools for Petri nets emerged, offering various analytical algorithms. From this follows a problem of using different programs to analyse a single model. Many file formats and different representations of results make the analysis much harder. Especially for larger nets the ability to visualize the results in a proper form provides a huge help in the understanding of their significance. We present a new tool for Petri nets development and analysis called Holmes. Our program contains algorithms for model analysis based on different types of Petri nets, e.g. invariant generator, Maximum Common Transitions (MCT) sets and cluster modules, simulation algorithms or knockout analysis tools. A very important feature is the ability to visualize the results of almost all analytical modules. The integration of such modules into one graphical environment allows a researcher to fully devote his or her time to the model building and analysis. Available at http://www.cs.put.poznan.pl/mradom/Holmes/holmes.html. piotr@cs.put.poznan.pl. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Robustness analysis of non-ordinary Petri nets for flexible assembly systems

NASA Astrophysics Data System (ADS)

Hsieh, Fu-Shiung

2010-05-01

Non-ordinary controlled Petri nets (NCPNs) have the advantages to model flexible assembly systems in which multiple identical resources may be required to perform an operation. However, existing studies on NCPNs are still limited. For example, the robustness properties of NCPNs have not been studied. This motivates us to develop an analysis method for NCPNs. Robustness analysis concerns the ability for a system to maintain operation in the presence of uncertainties. It provides an alternative way to analyse a perturbed system without reanalysis. In our previous research, we have analysed the robustness properties of several subclasses of ordinary controlled Petri nets. To study the robustness properties of NCPNs, we augment NCPNs with an uncertainty model, which specifies an upper bound on the uncertainties for each reachable marking. The resulting PN models are called non-ordinary controlled Petri nets with uncertainties (NCPNU). Based on NCPNU, the problem is to characterise the maximal tolerable uncertainties for each reachable marking. The computational complexities to characterise maximal tolerable uncertainties for each reachable marking grow exponentially with the size of the nets. Instead of considering general NCPNU, we limit our scope to a subclass of PN models called non-ordinary controlled flexible assembly Petri net with uncertainties (NCFAPNU) for assembly systems and study its robustness. We will extend the robustness analysis to NCFAPNU. We identify two types of uncertainties under which the liveness of NCFAPNU can be maintained.

Biopathways representation and simulation on hybrid functional petri net.

PubMed

Matsuno, Hiroshi; Tanaka, Yukiko; Aoshima, Hitoshi; Doi, Atsushi; Matsui, Mika; Miyano, Satoru

2011-01-01

The following two matters should be resolved in order for biosimulation tools to be accepted by users in biology/medicine: (1) remove issues which are irrelevant to biological importance, and (2) allow users to represent biopathways intuitively and understand/manage easily the details of representation and simulation mechanism. From these criteria, we firstly define a novel notion of Petri net called Hybrid Functional Petri Net (HFPN). Then, we introduce a software tool, Genomic Object Net, for representing and simulating biopathways, which we have developed by employing the architecture of HFPN. In order to show the usefulness of Genomic Object Net for representing and simulating biopathways, we show two HFPN representations of gene regulation mechanisms of Drosophila melanogaster (fruit fly) circadian rhythm and apoptosis induced by Fas ligand. The simulation results of these biopathways are also correlated with biological observations. The software is available to academic users from http://www.GenomicObject.Net/.

Model-based occluded object recognition using Petri nets

NASA Astrophysics Data System (ADS)

Zhou, Chuan; Hura, Gurdeep S.

1998-09-01

This paper discusses the use of Petri nets to model the process of the object matching between an image and a model under different 2D geometric transformations. This transformation finds its applications in sensor-based robot control, flexible manufacturing system and industrial inspection, etc. A description approach for object structure is presented by its topological structure relation called Point-Line Relation Structure (PLRS). It has been shown how Petri nets can be used to model the matching process, and an optimal or near optimal matching can be obtained by tracking the reachability graph of the net. The experiment result shows that object can be successfully identified and located under 2D transformation such as translations, rotations, scale changes and distortions due to object occluded partially.

A model of airport security work flow based on petri net

NASA Astrophysics Data System (ADS)

Dong, Xinming

2017-09-01

Extremely long lines at airports in the United States have been sharply criticized. In order to find out the bottleneck in the existing security system and put forward reasonable improvement plans and proposal, the Petri net model and the Markov Chain are introduced in this paper. This paper uses data collected by transportation Security Agency (TSA), assuming the data can represent the average level of all airports in the Unites States, to analysis the performance of security check system. By calculating the busy probabilities and the utilization probabilities, the bottleneck is found. Moreover, recommendation is given based on the parameters’ modification in Petri net model.

Gradient-based controllers for timed continuous Petri nets

NASA Astrophysics Data System (ADS)

Lefebvre, Dimitri; Leclercq, Edouard; Druaux, Fabrice; Thomas, Philippe

2015-07-01

This paper is about control design for timed continuous Petri nets that are described as piecewise affine systems. In this context, the marking vector is considered as the state space vector, weighted marking of place subsets are defined as the model outputs and the model inputs correspond to multiplicative control actions that slow down the firing rate of some controllable transitions. Structural and functional sensitivity of the outputs with respect to the inputs are discussed in terms of Petri nets. Then, gradient-based controllers (GBC) are developed in order to adapt the control actions of the controllable transitions according to desired trajectories of the outputs.

Hemojuvelin-hepcidin axis modeled and analyzed using Petri nets.

PubMed

Formanowicz, Dorota; Kozak, Adam; Głowacki, Tomasz; Radom, Marcin; Formanowicz, Piotr

2013-12-01

Systems biology approach to investigate biological phenomena seems to be very promising because it is capable to capture one of the fundamental properties of living organisms, i.e. their inherent complexity. It allows for analysis biological entities as complex systems of interacting objects. The first and necessary step of such an analysis is building a precise model of the studied biological system. This model is expressed in the language of some branch of mathematics, as for example, differential equations. During the last two decades the theory of Petri nets has appeared to be very well suited for building models of biological systems. The structure of these nets reflects the structure of interacting biological molecules and processes. Moreover, on one hand, Petri nets have intuitive graphical representation being very helpful in understanding the structure of the system and on the other hand, there is a lot of mathematical methods and software tools supporting an analysis of the properties of the nets. In this paper a Petri net based model of the hemojuvelin-hepcidin axis involved in the maintenance of the human body iron homeostasis is presented. The analysis based mainly on T-invariants of the model properties has been made and some biological conclusions have been drawn. Copyright © 2013 Elsevier Inc. All rights reserved.

Information flow analysis and Petri-net-based modeling for welding flexible manufacturing cell

NASA Astrophysics Data System (ADS)

Qiu, T.; Chen, Shanben; Wang, Y. T.; Wu, Lin

2000-10-01

Due to the development of advanced manufacturing technology and the introduction of Smart-Manufacturing notion in the field of modern industrial production, welding flexible manufacturing system (WFMS) using robot technology has become the inevitable developing direction on welding automation. In WFMS process, the flexibility for different welding products and the realizing on corresponding welding parameters control are the guarantees for welding quality. Based on a new intelligent arc-welding flexible manufacturing cell (WFMC), the system structure and control policies are studied in this paper. Aiming at the different information flows among every subsystem and central monitoring computer in this WFMC, Petri net theory is introduced into the process of welding manufacturing. With its help, a discrete control model of WFMC has been constructed, in which the system status is regarded as place and the control process is regarded as transition. Moreover, grounded on automation Petri net principle, the judging and utilizing of information obtained from welding sensors are imported into net structure, which extends the traditional Petri net concepts. The control model and policies researched in this paper have established foundation for further intelligent real-time control on WFMC and WFMS.

Virtual Control Policy for Binary Ordered Resources Petri Net Class.

PubMed

Rovetto, Carlos A; Concepción, Tomás J; Cano, Elia Esther

2016-08-18

Prevention and avoidance of deadlocks in sensor networks that use the wormhole routing algorithm is an active research domain. There are diverse control policies that will address this problem being our approach a new method. In this paper we present a virtual control policy for the new specialized Petri net subclass called Binary Ordered Resources Petri Net (BORPN). Essentially, it is an ordinary class constructed from various state machines that share unitary resources in a complex form, which allows branching and joining of processes. The reduced structure of this new class gives advantages that allow analysis of the entire system's behavior, which is a prohibitive task for large systems because of the complexity and routing algorithms.

Modeling and implementation of concurrent logic controllers with use of Petri nets, LSMs, and sequent calculus

NASA Astrophysics Data System (ADS)

Tkacz, J.; Bukowiec, A.; Doligalski, M.

2017-08-01

The paper presentes the method of modeling and implementation of concurrent controllers. Concurrent controllers are specified by Petri nets. Then Petri nets are decomposed using symbolic deduction method of analysis. Formal methods like sequent calculus system with considered elements of Thelen's algorithm have been used here. As a result, linked state machines (LSMs) are received. Each FSM is implemented using methods of structural decomposition during process of logic synthesis. The method of multiple encoding of microinstruction has been applied. It leads to decreased number of Boolean function realized by combinational part of FSM. The additional decoder could be implemented with the use of memory blocks.

Using Colored Stochastic Petri Net (CS-PN) software for protocol specification, validation, and evaluation

NASA Technical Reports Server (NTRS)

Zenie, Alexandre; Luguern, Jean-Pierre

1987-01-01

The specification, verification, validation, and evaluation, which make up the different steps of the CS-PN software are outlined. The colored stochastic Petri net software is applied to a Wound/Wait protocol decomposable into two principal modules: request or couple (transaction, granule) treatment module and wound treatment module. Each module is specified, verified, validated, and then evaluated separately, to deduce a verification, validation and evaluation of the complete protocol. The colored stochastic Petri nets tool is shown to be a natural extension of the stochastic tool, adapted to distributed systems and protocols, because the color conveniently takes into account the numerous sites, transactions, granules and messages.

Aspects regarding at 13C isotope separation column control using Petri nets system

NASA Astrophysics Data System (ADS)

Boca, M. L.; Ciortea, M. E.

2015-11-01

This paper is intended to show that Petri nets can be also applicable in the chemical industry. It used linear programming, modeling underlying Petri nets, especially discrete event systems for isotopic separation, the purpose of considering and control events in real-time through graphical representations. In this paper it is simulate the control of 13C Isotope Separation column using Petri nets. The major problem with 13C comes from the difficulty of obtaining it and raising its natural fraction. Carbon isotopes can be obtained using many methods, one of them being the cryogenic distillation of carbon monoxide. Some few aspects regarding operating conditions and the construction of such cryogenic plants are known today, and even less information are available as far as the separation process modeling and control are concerned. In fact, the efficient control of the carbon monoxide distillation process represents a necessity for large-scale 13C production. Referring to a classic distillation process, some models for carbon isotope separation have been proposed, some based on mass, component and energy balance equations, some on the nonlinear wave theory or the Cohen equations. For modeling the system it was used Petri nets because in this case it is deal with discrete event systems. In use of the non-timed and with auxiliary times Petri model, the transport stream was divided into sections and these sections will be analyzed successively. Because of the complexity of the system and the large amount of calculations required it was not possible to analyze the system as a unitary whole. A first attempt to model the system as a unitary whole led to the blocking of the model during simulation, because of the large processing times.

Modelling and analysis of workflow for lean supply chains

NASA Astrophysics Data System (ADS)

Ma, Jinping; Wang, Kanliang; Xu, Lida

2011-11-01

Cross-organisational workflow systems are a component of enterprise information systems which support collaborative business process among organisations in supply chain. Currently, the majority of workflow systems is developed in perspectives of information modelling without considering actual requirements of supply chain management. In this article, we focus on the modelling and analysis of the cross-organisational workflow systems in the context of lean supply chain (LSC) using Petri nets. First, the article describes the assumed conditions of cross-organisation workflow net according to the idea of LSC and then discusses the standardisation of collaborating business process between organisations in the context of LSC. Second, the concept of labelled time Petri nets (LTPNs) is defined through combining labelled Petri nets with time Petri nets, and the concept of labelled time workflow nets (LTWNs) is also defined based on LTPNs. Cross-organisational labelled time workflow nets (CLTWNs) is then defined based on LTWNs. Third, the article proposes the notion of OR-silent CLTWNS and a verifying approach to the soundness of LTWNs and CLTWNs. Finally, this article illustrates how to use the proposed method by a simple example. The purpose of this research is to establish a formal method of modelling and analysis of workflow systems for LSC. This study initiates a new perspective of research on cross-organisational workflow management and promotes operation management of LSC in real world settings.

Distributed intelligent scheduling of FMS

NASA Astrophysics Data System (ADS)

Wu, Zuobao; Cheng, Yaodong; Pan, Xiaohong

1995-08-01

In this paper, a distributed scheduling approach of a flexible manufacturing system (FMS) is presented. A new class of Petri nets called networked time Petri nets (NTPN) for system modeling of networking environment is proposed. The distributed intelligent scheduling is implemented by three schedulers which combine NTPN models with expert system techniques. The simulation results are shown.

Phenomenological and molecular-level Petri net modeling and simulation of long-term potentiation.

PubMed

Hardy, S; Robillard, P N

2005-10-01

Petri net-based modeling methods have been used in many research projects to represent biological systems. Among these, the hybrid functional Petri net (HFPN) was developed especially for biological modeling in order to provide biologists with a more intuitive Petri net-based method. In the literature, HFPNs are used to represent kinetic models at the molecular level. We present two models of long-term potentiation previously represented by differential equations which we have transformed into HFPN models: a phenomenological synapse model and a molecular-level model of the CaMKII regulation pathway. Through simulation, we obtained results similar to those of previous studies using these models. Our results open the way to a new type of modeling for systems biology where HFPNs are used to combine different levels of abstraction within one model. This approach can be useful in fully modeling a system at the molecular level when kinetic data is missing or when a full study of a system at the molecular level it is not within the scope of the research.

A colored petri nets based workload evaluation model and its validation through Multi-Attribute Task Battery-II.

PubMed

Wang, Peng; Fang, Weining; Guo, Beiyuan

2017-04-01

This paper proposed a colored petri nets based workload evaluation model. A formal interpretation of workload was firstly introduced based on the process that reflection of petri nets components to task. A petri net based description of Multiple Resources theory was given by comprehending it from a new angle. A new application of VACP rating scales named V/A-C-P unit, and the definition of colored transitions were proposed to build a model of task process. The calculation of workload mainly has the following four steps: determine token's initial position and values; calculate the weight of directed arcs on the basis of the rules proposed; calculate workload from different transitions, and correct the influence of repetitive behaviors. Verify experiments were carried out based on Multi-Attribute Task Battery-II software. Our results show that there is a strong correlation between the model values and NASA -Task Load Index scores (r=0.9513). In addition, this method can also distinguish behavior characteristics between different people. Copyright © 2016 Elsevier Ltd. All rights reserved.

Qualitatively modelling and analysing genetic regulatory networks: a Petri net approach.

PubMed

Steggles, L Jason; Banks, Richard; Shaw, Oliver; Wipat, Anil

2007-02-01

New developments in post-genomic technology now provide researchers with the data necessary to study regulatory processes in a holistic fashion at multiple levels of biological organization. One of the major challenges for the biologist is to integrate and interpret these vast data resources to gain a greater understanding of the structure and function of the molecular processes that mediate adaptive and cell cycle driven changes in gene expression. In order to achieve this biologists require new tools and techniques to allow pathway related data to be modelled and analysed as network structures, providing valuable insights which can then be validated and investigated in the laboratory. We propose a new technique for constructing and analysing qualitative models of genetic regulatory networks based on the Petri net formalism. We take as our starting point the Boolean network approach of treating genes as binary switches and develop a new Petri net model which uses logic minimization to automate the construction of compact qualitative models. Our approach addresses the shortcomings of Boolean networks by providing access to the wide range of existing Petri net analysis techniques and by using non-determinism to cope with incomplete and inconsistent data. The ideas we present are illustrated by a case study in which the genetic regulatory network controlling sporulation in the bacterium Bacillus subtilis is modelled and analysed. The Petri net model construction tool and the data files for the B. subtilis sporulation case study are available at http://bioinf.ncl.ac.uk/gnapn.

Application of modified Martinez-Silva algorithm in determination of net cover

NASA Astrophysics Data System (ADS)

Stefanowicz, Łukasz; Grobelna, Iwona

2016-12-01

In the article we present the idea of modifications of Martinez-Silva algorithm, which allows for determination of place invariants (p-invariants) of Petri net. Their generation time is important in the parallel decomposition of discrete systems described by Petri nets. Decomposition process is essential from the point of view of discrete system design, as it allows for separation of smaller sequential parts. The proposed modifications of Martinez-Silva method concern the net cover by p-invariants and are focused on two important issues: cyclic reduction of invariant matrix and cyclic checking of net cover.

Applying Dynamic Fuzzy Petri Net to Web Learning System

ERIC Educational Resources Information Center

Chen, Juei-Nan; Huang, Yueh-Min; Chu, William

2005-01-01

This investigation presents a DFPN (Dynamic Fuzzy Petri Net) model to increase the flexibility of the tutoring agent's behaviour and thus provide a learning content structure for a lecture course. The tutoring agent is a software assistant for a single user, who may be an expert in an e-Learning course. Based on each learner's behaviour, the…

Models of the Behavior of People Searching the Internet: A Petri Net Approach.

ERIC Educational Resources Information Center

Kantor, Paul B.; Nordlie, Ragnar

1999-01-01

Illustrates how various key abstractions of information finding, such as document relevance, a desired number of relevant documents, discouragement, exhaustion, and satisfaction can be modeled using the Petri Net framework. Shows that this model leads naturally to a new approach to collection of user data, and to analysis of transaction logs.…

Threat driven modeling framework using petri nets for e-learning system.

PubMed

Khamparia, Aditya; Pandey, Babita

2016-01-01

Vulnerabilities at various levels are main cause of security risks in e-learning system. This paper presents a modified threat driven modeling framework, to identify the threats after risk assessment which requires mitigation and how to mitigate those threats. To model those threat mitigations aspects oriented stochastic petri nets are used. This paper included security metrics based on vulnerabilities present in e-learning system. The Common Vulnerability Scoring System designed to provide a normalized method for rating vulnerabilities which will be used as basis in metric definitions and calculations. A case study has been also proposed which shows the need and feasibility of using aspect oriented stochastic petri net models for threat modeling which improves reliability, consistency and robustness of the e-learning system.

Modeling of wastewater treatment system of car parks from petroleum products

NASA Astrophysics Data System (ADS)

Savdur, S. N.; Stepanova, Yu V.; Kodolova, I. A.; Fesina, E. L.

2018-05-01

The paper discusses the technological complex of wastewater treatment of car parks from petroleum products. Based on the review of the main modeling methods of discrete-continuous chemical and engineering processes, it substantiates expediency of using the theory of Petri nets (PN) for modeling the process of wastewater treatment of car parks from petroleum products. It is proposed to use a modification of Petri nets which is focused on modeling and analysis of discrete-continuous chemical and engineering processes by prioritizing transitions, timing marks in positions and transitions. A model in the form of modified Petri nets (MPN) is designed. A software package to control the process for wastewater treatment is designed by means of SCADA TRACE MODE.

Discrete-time Markovian stochastic Petri nets

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco

1995-01-01

We revisit and extend the original definition of discrete-time stochastic Petri nets, by allowing the firing times to have a 'defective discrete phase distribution'. We show that this formalism still corresponds to an underlying discrete-time Markov chain. The structure of the state for this process describes both the marking of the Petri net and the phase of the firing time for each transition, resulting in a large state space. We then modify the well-known power method to perform a transient analysis even when the state space is infinite, subject to the condition that only a finite number of states can be reached in a finite amount of time. Since the memory requirements might still be excessive, we suggest a bounding technique based on truncation.

Applying a semantic information Petri Net modeling method to AUV systems design

NASA Astrophysics Data System (ADS)

Feng, Xiao-Ning; Wang, Shuo; Wang, Zhuo; Liu, Qun

2008-12-01

This paper informally introduces colored object-oriented Petri Nets(COOPN) with the application of the AUV system. According to the characteristic of the AUV system’s running environment, the object-oriented method is used in this paper not only to dispart system modules but also construct the refined running model of AUV system, then the colored Petri Net method is used to establish hierarchically detailed model in order to get the performance analyzing information of the system. After analyzing the model implementation, the errors of architecture designing and function realization can be found. If the errors can be modified on time, the experiment time in the pool can be reduced and the cost can be saved.

Virtual Control Policy for Binary Ordered Resources Petri Net Class

PubMed Central

Rovetto, Carlos A.; Concepción, Tomás J.; Cano, Elia Esther

2016-01-01

Prevention and avoidance of deadlocks in sensor networks that use the wormhole routing algorithm is an active research domain. There are diverse control policies that will address this problem being our approach a new method. In this paper we present a virtual control policy for the new specialized Petri net subclass called Binary Ordered Resources Petri Net (BORPN). Essentially, it is an ordinary class constructed from various state machines that share unitary resources in a complex form, which allows branching and joining of processes. The reduced structure of this new class gives advantages that allow analysis of the entire system’s behavior, which is a prohibitive task for large systems because of the complexity and routing algorithms. PMID:27548170

A Petri-net coordination model for an intelligent mobile robot

NASA Technical Reports Server (NTRS)

Wang, F.-Y.; Kyriakopoulos, K. J.; Tsolkas, A.; Saridis, G. N.

1990-01-01

The authors present a Petri net model of the coordination level of an intelligent mobile robot system (IMRS). The purpose of this model is to specify the integration of the individual efforts on path planning, supervisory motion control, and vision systems that are necessary for the autonomous operation of the mobile robot in a structured dynamic environment. This is achieved by analytically modeling the various units of the system as Petri net transducers and explicitly representing the task precedence and information dependence among them. The model can also be used to simulate the task processing and to evaluate the efficiency of operations and the responsibility of decisions in the coordination level of the IMRS. Some simulation results on the task processing and learning are presented.

Petri net modelling of gene regulation of the Duchenne muscular dystrophy.

PubMed

Grunwald, Stefanie; Speer, Astrid; Ackermann, Jörg; Koch, Ina

2008-05-01

Searching for therapeutic strategies for Duchenne muscular dystrophy, it is of great interest to understand the responsible molecular pathways down-stream of dystrophin completely. For this reason we have performed real-time PCR experiments to compare mRNA expression levels of relevant genes in tissues of affected patients and controls. To bring experimental data in context with the underlying pathway theoretical models are needed. Modelling of biological processes in the cell at higher description levels is still an open problem in the field of systems biology. In this paper, a new application of Petri net theory is presented to model gene regulatory processes of Duchenne muscular dystrophy. We have developed a Petri net model, which is based mainly on own experimental and literature data. We distinguish between up- and down-regulated states of gene expression. The analysis of the model comprises the computation of structural and dynamic properties with focus on a thorough T-invariant analysis, including clustering techniques and the decomposition of the network into maximal common transition sets (MCT-sets), which can be interpreted as functionally related building blocks. All possible pathways, which reflect the complex net behaviour in dependence of different gene expression patterns, are discussed. We introduce Mauritius maps of T-invariants, which enable, for example, theoretical knockout analysis. The resulted model serves as basis for a better understanding of pathological processes, and thereby for planning next experimental steps in searching for new therapeutic possibilities. Free availability of the Petri net editor and animator Snoopy and the clustering tool PInA via http://www-dssz.informatik.tu-cottbus.de/~ wwwdssz/. The Petri net models used can be accessed via http://www.tfh-berlin.de/bi/duchenne/.

Stochastic Petri Net Modeling of Wave Sequences in Cardiac Arrhythmias.

DTIC Science & Technology

1987-11-01

Wolff - Parkinson - White syndrome . The ventricles are divided into two parts. One of these is excited normally and produces R...example, in a condition called the Wolff - Parkinson - White syn- drome the ECG displays an abnormally early onset of the ventricular activity. It also...8217. , ’ ", -’ , .’ %,,? .’ ,; ’ .- ’ ’ -’ € ’ , . ’ - I. 32 Wolfe- Parkinson - White Syndrome (Fig. 8c) This model uses "basic" elements for the

Industry Strength Tool and Technology for Automated Synthesis of Safety-Critical Applications from Formal Specifications

DTIC Science & Technology

2015-11-01

28 2.3.4 Input/Output Automata ...various other modeling frameworks such as I/O Automata , Kahn Process Networks, Petri-nets, Multi-dimensional SDF, etc. are also used for designing...Formal Ideally suited to model DSP applications 3 Petri Nets Graphical Formal Used for modeling distributed systems 4 I/O Automata Both Formal

Reachability analysis of real-time systems using time Petri nets.

PubMed

Wang, J; Deng, Y; Xu, G

2000-01-01

Time Petri nets (TPNs) are a popular Petri net model for specification and verification of real-time systems. A fundamental and most widely applied method for analyzing Petri nets is reachability analysis. The existing technique for reachability analysis of TPNs, however, is not suitable for timing property verification because one cannot derive end-to-end delay in task execution, an important issue for time-critical systems, from the reachability tree constructed using the technique. In this paper, we present a new reachability based analysis technique for TPNs for timing property analysis and verification that effectively addresses the problem. Our technique is based on a concept called clock-stamped state class (CS-class). With the reachability tree generated based on CS-classes, we can directly compute the end-to-end time delay in task execution. Moreover, a CS-class can be uniquely mapped to a traditional state class based on which the conventional reachability tree is constructed. Therefore, our CS-class-based analysis technique is more general than the existing technique. We show how to apply this technique to timing property verification of the TPN model of a command and control (C2) system.

Formalization, implementation, and modeling of institutional controllers for distributed robotic systems.

PubMed

Pereira, José N; Silva, Porfírio; Lima, Pedro U; Martinoli, Alcherio

2014-01-01

The work described is part of a long term program of introducing institutional robotics, a novel framework for the coordination of robot teams that stems from institutional economics concepts. Under the framework, institutions are cumulative sets of persistent artificial modifications made to the environment or to the internal mechanisms of a subset of agents, thought to be functional for the collective order. In this article we introduce a formal model of institutional controllers based on Petri nets. We define executable Petri nets-an extension of Petri nets that takes into account robot actions and sensing-to design, program, and execute institutional controllers. We use a generalized stochastic Petri net view of the robot team controlled by the institutional controllers to model and analyze the stochastic performance of the resulting distributed robotic system. The ability of our formalism to replicate results obtained using other approaches is assessed through realistic simulations of up to 40 e-puck robots. In particular, we model a robot swarm and its institutional controller with the goal of maintaining wireless connectivity, and successfully compare our model predictions and simulation results with previously reported results, obtained by using finite state automaton models and controllers.

Decentralised control of continuous Petri nets

NASA Astrophysics Data System (ADS)

Wang, Liewei; Wang, Xu

2017-05-01

This paper focuses on decentralised control of systems modelled by continuous Petri nets, in which a target marking control problem is discussed. In some previous works, an efficient ON/OFF strategy-based minimum-time controller was developed. Nevertheless, the convergence is only proved for subclasses like Choice-Free nets. For a general net, the pre-conditions of applying the ON/OFF strategy are not given; therefore, the application scope of the method is unclear. In this work, we provide two sufficient conditions of applying the ON/OFF strategy-based controller to general nets. Furthermore, an extended algorithm for general nets is proposed, in which control laws are computed based on some limited information, without knowing the detailed structure of subsystems.

Petri net modelling of buffers in automated manufacturing systems.

PubMed

Zhou, M; Dicesare, F

1996-01-01

This paper presents Petri net models of buffers and a methodology by which buffers can be included in a system without introducing deadlocks or overflows. The context is automated manufacturing. The buffers and models are classified as random order or order preserved (first-in-first-out or last-in-first-out), single-input-single-output or multiple-input-multiple-output, part type and/or space distinguishable or indistinguishable, and bounded or safe. Theoretical results for the development of Petri net models which include buffer modules are developed. This theory provides the conditions under which the system properties of boundedness, liveness, and reversibility are preserved. The results are illustrated through two manufacturing system examples: a multiple machine and multiple buffer production line and an automatic storage and retrieval system in the context of flexible manufacturing.

Runtime Verification of Pacemaker Functionality Using Hierarchical Fuzzy Colored Petri-nets.

PubMed

Majma, Negar; Babamir, Seyed Morteza; Monadjemi, Amirhassan

2017-02-01

Today, implanted medical devices are increasingly used for many patients and in case of diverse health problems. However, several runtime problems and errors are reported by the relevant organizations, even resulting in patient death. One of those devices is the pacemaker. The pacemaker is a device helping the patient to regulate the heartbeat by connecting to the cardiac vessels. This device is directed by its software, so any failure in this software causes a serious malfunction. Therefore, this study aims to a better way to monitor the device's software behavior to decrease the failure risk. Accordingly, we supervise the runtime function and status of the software. The software verification means examining limitations and needs of the system users by the system running software. In this paper, a method to verify the pacemaker software, based on the fuzzy function of the device, is presented. So, the function limitations of the device are identified and presented as fuzzy rules and then the device is verified based on the hierarchical Fuzzy Colored Petri-net (FCPN), which is formed considering the software limits. Regarding the experiences of using: 1) Fuzzy Petri-nets (FPN) to verify insulin pumps, 2) Colored Petri-nets (CPN) to verify the pacemaker and 3) To verify the pacemaker by a software agent with Petri-network based knowledge, which we gained during the previous studies, the runtime behavior of the pacemaker software is examined by HFCPN, in this paper. This is considered a developing step compared to the earlier work. HFCPN in this paper, compared to the FPN and CPN used in our previous studies reduces the complexity. By presenting the Petri-net (PN) in a hierarchical form, the verification runtime, decreased as 90.61% compared to the verification runtime in the earlier work. Since we need an inference engine in the runtime verification, we used the HFCPN to enhance the performance of the inference engine.

Hardware implementation of fuzzy Petri net as a controller.

PubMed

Gniewek, Lesław; Kluska, Jacek

2004-06-01

The paper presents a new approach to fuzzy Petri net (FPN) and its hardware implementation. The authors' motivation is as follows. Complex industrial processes can be often decomposed into many parallelly working subprocesses, which can, in turn, be modeled using Petri nets. If all the process variables (or events) are assumed to be two-valued signals, then it is possible to obtain a hardware or software control device, which works according to the algorithm described by conventional Petri net. However, the values of real signals are contained in some bounded interval and can be interpreted as events which are not only true or false, but rather true in some degree from the interval [0, 1]. Such a natural interpretation from multivalued logic (fuzzy logic) point of view, concerns sensor outputs, control signals, time expiration, etc. It leads to the idea of FPN as a controller, which one can rather simply obtain, and which would be able to process both analog, and binary signals. In the paper both graphical, and algebraic representations of the proposed FPN are given. The conditions under which transitions can be fired are described. The algebraic description of the net and a theorem which enables computation of new marking in the net, based on current marking, are formulated. Hardware implementation of the FPN, which uses fuzzy JK flip-flops and fuzzy gates, are proposed. An example illustrating usefulness of the proposed FPN for control algorithm description and its synthesis as a controller device for the concrete production process are presented.

Neural networks with fuzzy Petri nets for modeling a machining process

NASA Astrophysics Data System (ADS)

Hanna, Moheb M.

1998-03-01

The paper presents an intelligent architecture based a feedforward neural network with fuzzy Petri nets for modeling product quality in a CNC machining center. It discusses how the proposed architecture can be used for modeling, monitoring and control a product quality specification such as surface roughness. The surface roughness represents the output quality specification manufactured by a CNC machining center as a result of a milling process. The neural network approach employed the selected input parameters which defined by the machine operator via the CNC code. The fuzzy Petri nets approach utilized the exact input milling parameters, such as spindle speed, feed rate, tool diameter and coolant (off/on), which can be obtained via the machine or sensors system. An aim of the proposed architecture is to model the demanded quality of surface roughness as high, medium or low.

A distributed Petri Net controller for a dual arm testbed

NASA Technical Reports Server (NTRS)

Bjanes, Atle

1991-01-01

This thesis describes the design and functionality of a Distributed Petri Net Controller (DPNC). The controller runs under X Windows to provide a graphical interface. The DPNC allows users to distribute a Petri Net across several host computers linked together via a TCP/IP interface. A sub-net executes on each host, interacting with the other sub-nets by passing a token vector from host to host. One host has a command window which monitors and controls the distributed controller. The input to the DPNC is a net definition file generated by Great SPN. Thus, a net may be designed, analyzed and verified using this package before implementation. The net is distributed to the hosts by tagging transitions that are host-critical with the appropriate host number. The controller will then distribute the remaining places and transitions to the hosts by generating the local nets, the local marking vectors and the global marking vector. Each transition can have one or more preconditions which must be fulfilled before the transition can fire, as well as one or more post-processes to be executed after the transition fires. These implement the actual input/output to the environment (machines, signals, etc.). The DPNC may also be used to simulate a Great SPN net since stochastic and deterministic firing rates are implemented in the controller for timed transitions.

Petri net model for analysis of concurrently processed complex algorithms

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Mielke, Roland R.

1986-01-01

This paper presents a Petri-net model suitable for analyzing the concurrent processing of computationally complex algorithms. The decomposed operations are to be processed in a multiple processor, data driven architecture. Of particular interest is the application of the model to both the description of the data/control flow of a particular algorithm, and to the general specification of the data driven architecture. A candidate architecture is also presented.

Developmental switching in Physarum polycephalum: Petri net analysis of single cell trajectories of gene expression indicates responsiveness and genetic plasticity of the Waddington quasipotential landscape

NASA Astrophysics Data System (ADS)

Werthmann, Britta; Marwan, Wolfgang

2017-11-01

The developmental switch to sporulation in Physarum polycephalum is a phytochrome-mediated far-red light-induced cell fate decision that synchronously encompasses the entire multinucleate plasmodial cell and is associated with extensive reprogramming of the transcriptome. By repeatedly taking samples of single cells after delivery of a light stimulus pulse, we analysed differential gene expression in two mutant strains and in a heterokaryon of the two strains all of which display a different propensity for making the cell fate decision. Multidimensional scaling of the gene expression data revealed individually different single cell trajectories eventually leading to sporulation. Characterization of the trajectories as walks through states of gene expression discretized by hierarchical clustering allowed the reconstruction of Petri nets that model and predict the observed behavior. Structural analyses of the Petri nets indicated stimulus- and genotype-dependence of both, single cell trajectories and of the quasipotential landscape through which these trajectories are taken. The Petri net-based approach to the analysis and decomposition of complex cellular responses and of complex mutant phenotypes may provide a scaffold for the data-driven reconstruction of causal molecular mechanisms that shape the topology of the quasipotential landscape.

Extension of the lower bound of monitor solutions of maximally permissive supervisors to non-α net systems

NASA Astrophysics Data System (ADS)

Wu, W. H.; Chao, D. Y.

2016-07-01

Traditional region-based liveness-enforcing supervisors focus on (1) maximal permissiveness of not losing legal states, (2) structural simplicity of minimal number of monitors, and (3) fast computation. Lately, a number of similar approaches can achieve minimal configuration using efficient linear programming. However, it is unclear as to the relationship between the minimal configuration and the net structure. It is important to explore the structures involved for the fewest monitors required. Once the lower bound is achieved, further iteration to merge (or reduce the number of) monitors is not necessary. The minimal strongly connected resource subnet (i.e., all places are resources) that contains the set of resource places in a basic siphon is an elementary circuit. Earlier, we showed that the number of monitors required for liveness-enforcing and maximal permissiveness equals that of basic siphons for a subclass of Petri nets modelling manufacturing, called α systems. This paper extends this to systems more powerful than the α one so that the number of monitors in a minimal configuration remains to be lower bounded by that of basic siphons. This paper develops the theory behind and shows examples.

Design and verification of distributed logic controllers with application of Petri nets

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wiśniewski, Remigiusz; Grobelna, Iwona; Grobelny, Michał

2015-12-31

The paper deals with the designing and verification of distributed logic controllers. The control system is initially modelled with Petri nets and formally verified against structural and behavioral properties with the application of the temporal logic and model checking technique. After that it is decomposed into separate sequential automata that are working concurrently. Each of them is re-verified and if the validation is successful, the system can be finally implemented.

Research on user behavior authentication model based on stochastic Petri nets

NASA Astrophysics Data System (ADS)

Zhang, Chengyuan; Xu, Haishui

2017-08-01

A behavioural authentication model based on stochastic Petri net is proposed to meet the randomness, uncertainty and concurrency characteristics of user behaviour. The use of random models in the location, changes, arc and logo to describe the characteristics of a variety of authentication and game relationships, so as to effectively implement the graphical user behaviour authentication model analysis method, according to the corresponding proof to verify the model is valuable.

Design and verification of distributed logic controllers with application of Petri nets

NASA Astrophysics Data System (ADS)

Wiśniewski, Remigiusz; Grobelna, Iwona; Grobelny, Michał; Wiśniewska, Monika

2015-12-01

The paper deals with the designing and verification of distributed logic controllers. The control system is initially modelled with Petri nets and formally verified against structural and behavioral properties with the application of the temporal logic and model checking technique. After that it is decomposed into separate sequential automata that are working concurrently. Each of them is re-verified and if the validation is successful, the system can be finally implemented.

Multi-tasking arbitration and behaviour design for human-interactive robots

NASA Astrophysics Data System (ADS)

Kobayashi, Yuichi; Onishi, Masaki; Hosoe, Shigeyuki; Luo, Zhiwei

2013-05-01

Robots that interact with humans in household environments are required to handle multiple real-time tasks simultaneously, such as carrying objects, collision avoidance and conversation with human. This article presents a design framework for the control and recognition processes to meet these requirements taking into account stochastic human behaviour. The proposed design method first introduces a Petri net for synchronisation of multiple tasks. The Petri net formulation is converted to Markov decision processes and processed in an optimal control framework. Three tasks (safety confirmation, object conveyance and conversation) interact and are expressed by the Petri net. Using the proposed framework, tasks that normally tend to be designed by integrating many if-then rules can be designed in a systematic manner in a state estimation and optimisation framework from the viewpoint of the shortest time optimal control. The proposed arbitration method was verified by simulations and experiments using RI-MAN, which was developed for interactive tasks with humans.

Health Monitoring of a Planetary Rover Using Hybrid Particle Petri Nets

NASA Technical Reports Server (NTRS)

Gaudel, Quentin; Ribot, Pauline; Chanthery, Elodie; Daigle, Matthew J.

2016-01-01

This paper focuses on the application of a Petri Net-based diagnosis method on a planetary rover prototype.The diagnosis is performed by using a model-based method in the context of health management of hybrid systems.In system health management, the diagnosis task aims at determining the current health state of a system and the fault occurrences that lead to this state. The Hybrid Particle Petri Nets (HPPN) formalism is used to model hybrid systems behavior and degradation, and to define the generation of diagnosers to monitor the health states of such systems under uncertainty. At any time, the HPPN-based diagnoser provides the current diagnosis represented by a distribution of beliefs over the health states. The health monitoring methodology is demonstrated on the K11 rover. A hybrid model of the K11 is proposed and experimental results show that the approach is robust to real system data and constraints.

Petri Net controller synthesis based on decomposed manufacturing models.

PubMed

Dideban, Abbas; Zeraatkar, Hashem

2018-06-01

Utilizing of supervisory control theory on the real systems in many modeling tools such as Petri Net (PN) becomes challenging in recent years due to the significant states in the automata models or uncontrollable events. The uncontrollable events initiate the forbidden states which might be removed by employing some linear constraints. Although there are many methods which have been proposed to reduce these constraints, enforcing them to a large-scale system is very difficult and complicated. This paper proposes a new method for controller synthesis based on PN modeling. In this approach, the original PN model is broken down into some smaller models in which the computational cost reduces significantly. Using this method, it is easy to reduce and enforce the constraints to a Petri net model. The appropriate results of our proposed method on the PN models denote worthy controller synthesis for the large scale systems. Copyright © 2018 ISA. Published by Elsevier Ltd. All rights reserved.

Coloured Logic Petri Nets and analysis of their reachable trees

NASA Astrophysics Data System (ADS)

Wang, Jing; Du, YuYue; Yu, ShuXia

2015-11-01

Logic Petri nets (LPNs) can describe and analyse the batch processing function and passing value indeterminacy in cooperative systems, and alleviate the state space explosion problem. However, the indeterminate data of logical output transitions cannot be described explicitly in LPNs. Therefore, Coloured Logic Petri nets (CLPNs) are defined in this paper. It can determine the indeterminate data of logic output transitions in LPNs, i.e., the indeterminate data can be represented definitely in CLPNs. A vector matching method is proposed to judge the enabling transitions and analyse CLPNs. From the marking equation and the proposed reachable tree generation algorithm of CLPNs, a reachable tree can be built, and reachable markings are calculated. The advantage of CLPNs can be shown based on the number of leaf nodes of the reachability tree, and CLPNs can solve the indeterminate data of logical output transitions. Finally, an example shows that CLPNs can further reduce the dimensionality of reachable markings.

Some aspects of the anemia of chronic disorders modeled and analyzed by petri net based approach.

PubMed

Formanowicz, Dorota; Sackmann, Andrea; Kozak, Adam; Błażewicz, Jacek; Formanowicz, Piotr

2011-06-01

Anemia of chronic disorders is a very important phenomenon and iron is a crucial factor of this complex process. To better understand this process and its influence on some other factors we have built a mathematical model of the human body iron homeostasis, which possibly most exactly would reflect the metabolism of iron in the case of anemia and inflammation. The model has been formulated in the language of Petri net theory, which allows for its simulation and precise analysis. The obtained results of the analysis of the model's behavior, concerning the influence of anemia and inflammation on the transferrin receptors, and hepcidin concentration changes are the valuable complements to the knowledge following from clinical research. This analysis is one of the first attempts to investigate properties and behavior of a not fully understood biological system on a basis of its Petri net based model.

A Design Verification of the Parallel Pipelined Image Processings

NASA Astrophysics Data System (ADS)

Wasaki, Katsumi; Harai, Toshiaki

2008-11-01

This paper presents a case study of the design and verification of a parallel and pipe-lined image processing unit based on an extended Petri net, which is called a Logical Colored Petri net (LCPN). This is suitable for Flexible-Manufacturing System (FMS) modeling and discussion of structural properties. LCPN is another family of colored place/transition-net(CPN) with the addition of the following features: integer value assignment of marks, representation of firing conditions as marks' value based formulae, and coupling of output procedures with transition firing. Therefore, to study the behavior of a system modeled with this net, we provide a means of searching the reachability tree for markings.

Applying generalized stochastic Petri nets to manufacturing systems containing nonexponential transition functions

NASA Technical Reports Server (NTRS)

Watson, James F., III; Desrochers, Alan A.

1991-01-01

Generalized stochastic Petri nets (GSPNs) are applied to flexible manufacturing systems (FMSs). Throughput subnets and s-transitions are presented. Two FMS examples containing nonexponential distributions which were analyzed in previous papers by queuing theory and probability theory, respectively, are treated using GSPNs developed using throughput subnets and s-transitions. The GSPN results agree with the previous results, and developing and analyzing the GSPN models are straightforward and relatively easy compared to other methodologies.

Petri Nets as Modeling Tool for Emergent Agents

NASA Technical Reports Server (NTRS)

Bergman, Marto

2004-01-01

Emergent agents, those agents whose local interactions can cause unexpected global results, require a method of modeling that is both dynamic and structured Petri Nets, a modeling tool developed for dynamic discrete event system of mainly functional agents, provide this, and have the benefit of being an established tool. We present here the details of the modeling method here and discuss how to implement its use for modeling agent-based systems. Petri Nets have been used extensively in the modeling of functional agents, those agents who have defined purposes and whose actions should result in a know outcome. However, emergent agents, those agents who have a defined structure but whose interaction causes outcomes that are unpredictable, have not yet found a modeling style that suits them. A problem with formally modeling emergent agents that any formal modeling style usually expects to show the results of a problem and the results of problems studied using emergent agents are not apparent from the initial construction. However, the study of emergent agents still requires a method to analyze the agents themselves, and have sensible conversation about the differences and similarities between types of emergent agents. We attempt to correct this problem by applying Petri Nets to the characterization of emergent agents. In doing so, the emergent properties of these agents can be highlighted, and conversation about the nature and compatibility of the differing methods of agent creation can begin.

Fuzzy Stochastic Petri Nets for Modeling Biological Systems with Uncertain Kinetic Parameters

PubMed Central

Liu, Fei; Heiner, Monika; Yang, Ming

2016-01-01

Stochastic Petri nets (SPNs) have been widely used to model randomness which is an inherent feature of biological systems. However, for many biological systems, some kinetic parameters may be uncertain due to incomplete, vague or missing kinetic data (often called fuzzy uncertainty), or naturally vary, e.g., between different individuals, experimental conditions, etc. (often called variability), which has prevented a wider application of SPNs that require accurate parameters. Considering the strength of fuzzy sets to deal with uncertain information, we apply a specific type of stochastic Petri nets, fuzzy stochastic Petri nets (FSPNs), to model and analyze biological systems with uncertain kinetic parameters. FSPNs combine SPNs and fuzzy sets, thereby taking into account both randomness and fuzziness of biological systems. For a biological system, SPNs model the randomness, while fuzzy sets model kinetic parameters with fuzzy uncertainty or variability by associating each parameter with a fuzzy number instead of a crisp real value. We introduce a simulation-based analysis method for FSPNs to explore the uncertainties of outputs resulting from the uncertainties associated with input parameters, which works equally well for bounded and unbounded models. We illustrate our approach using a yeast polarization model having an infinite state space, which shows the appropriateness of FSPNs in combination with simulation-based analysis for modeling and analyzing biological systems with uncertain information. PMID:26910830

Reconstruction of extended Petri nets from time series data and its application to signal transduction and to gene regulatory networks

PubMed Central

2011-01-01

Background Network inference methods reconstruct mathematical models of molecular or genetic networks directly from experimental data sets. We have previously reported a mathematical method which is exclusively data-driven, does not involve any heuristic decisions within the reconstruction process, and deliveres all possible alternative minimal networks in terms of simple place/transition Petri nets that are consistent with a given discrete time series data set. Results We fundamentally extended the previously published algorithm to consider catalysis and inhibition of the reactions that occur in the underlying network. The results of the reconstruction algorithm are encoded in the form of an extended Petri net involving control arcs. This allows the consideration of processes involving mass flow and/or regulatory interactions. As a non-trivial test case, the phosphate regulatory network of enterobacteria was reconstructed using in silico-generated time-series data sets on wild-type and in silico mutants. Conclusions The new exact algorithm reconstructs extended Petri nets from time series data sets by finding all alternative minimal networks that are consistent with the data. It suggested alternative molecular mechanisms for certain reactions in the network. The algorithm is useful to combine data from wild-type and mutant cells and may potentially integrate physiological, biochemical, pharmacological, and genetic data in the form of a single model. PMID:21762503

Liveness-enforcing supervisors synthesis for a class of generalised Petri nets based on two-stage deadlock control and mathematical programming

NASA Astrophysics Data System (ADS)

Zhao, Mi; Hou, Yifan; Liu, Ding

2010-10-01

In this article we deal with deadlock prevention problems for S4PR, a class of generalised Petri nets, which can well model a large class of flexible manufacturing systems where deadlocks are caused by insufficiently marked siphons. We present a deadlock prevention methodology that is an iterative approach consisting of two stages. The first one is called siphon control, which is to add for each insufficiently marked minimal siphon a control place to the original net. Its objective is to prevent a minimal siphon from being insufficiently marked. The second one, called control-induced siphon control, is to add a control place to the augmented net with its output arcs connecting to the source transitions, which assures that there are no new insufficiently marked siphons generated. At each iteration, a mixed integer programming approach is adopted for generalised Petri nets to obtain an insufficiently marked minimal siphon from the maximal deadly siphon. This way complete siphon enumeration is avoided that is much more time-consuming for a sizeable plant model than the proposed method. The relation of the proposed method and the liveness and reversibility of the controlled net is obtained. Examples are presented to demonstrate the presented method.

Petri net-based modelling of human-automation conflicts in aviation.

PubMed

Pizziol, Sergio; Tessier, Catherine; Dehais, Frédéric

2014-01-01

Analyses of aviation safety reports reveal that human-machine conflicts induced by poor automation design are remarkable precursors of accidents. A review of different crew-automation conflicting scenarios shows that they have a common denominator: the autopilot behaviour interferes with the pilot's goal regarding the flight guidance via 'hidden' mode transitions. Considering both the human operator and the machine (i.e. the autopilot or the decision functions) as agents, we propose a Petri net model of those conflicting interactions, which allows them to be detected as deadlocks in the Petri net. In order to test our Petri net model, we designed an autoflight system that was formally analysed to detect conflicting situations. We identified three conflicting situations that were integrated in an experimental scenario in a flight simulator with 10 general aviation pilots. The results showed that the conflicts that we had a-priori identified as critical had impacted the pilots' performance. Indeed, the first conflict remained unnoticed by eight participants and led to a potential collision with another aircraft. The second conflict was detected by all the participants but three of them did not manage the situation correctly. The last conflict was also detected by all the participants but provoked typical automation surprise situation as only one declared that he had understood the autopilot behaviour. These behavioural results are discussed in terms of workload and number of fired 'hidden' transitions. Eventually, this study reveals that both formal and experimental approaches are complementary to identify and assess the criticality of human-automation conflicts. Practitioner Summary: We propose a Petri net model of human-automation conflicts. An experiment was conducted with general aviation pilots performing a scenario involving three conflicting situations to test the soundness of our formal approach. This study reveals that both formal and experimental approaches are complementary to identify and assess the criticality conflicts.

A New Availability-Payment Model for Pricing Performance-Based Logistics Contracts

DTIC Science & Technology

2014-05-01

Petri   net ) is used to  capture concurrency and  synchronization...properties of the  system. Petri   Net Available IN 1`A failure indication IN Down Repair Shop IN Down Replace Order IN Replace Order U costs PC (1,2) time...action (expTime(50*w)); INT Repairs AV Replaces AV AV av.req AV DOWNTIME 0 INT 0 INT Manufacturer Quantity Inventory 5 Quantity stock Cost Book

High performance hybrid functional Petri net simulations of biological pathway models on CUDA.

PubMed

Chalkidis, Georgios; Nagasaki, Masao; Miyano, Satoru

2011-01-01

Hybrid functional Petri nets are a wide-spread tool for representing and simulating biological models. Due to their potential of providing virtual drug testing environments, biological simulations have a growing impact on pharmaceutical research. Continuous research advancements in biology and medicine lead to exponentially increasing simulation times, thus raising the demand for performance accelerations by efficient and inexpensive parallel computation solutions. Recent developments in the field of general-purpose computation on graphics processing units (GPGPU) enabled the scientific community to port a variety of compute intensive algorithms onto the graphics processing unit (GPU). This work presents the first scheme for mapping biological hybrid functional Petri net models, which can handle both discrete and continuous entities, onto compute unified device architecture (CUDA) enabled GPUs. GPU accelerated simulations are observed to run up to 18 times faster than sequential implementations. Simulating the cell boundary formation by Delta-Notch signaling on a CUDA enabled GPU results in a speedup of approximately 7x for a model containing 1,600 cells.

Task planning with uncertainty for robotic systems. Thesis

NASA Technical Reports Server (NTRS)

Cao, Tiehua

1993-01-01

In a practical robotic system, it is important to represent and plan sequences of operations and to be able to choose an efficient sequence from them for a specific task. During the generation and execution of task plans, different kinds of uncertainty may occur and erroneous states need to be handled to ensure the efficiency and reliability of the system. An approach to task representation, planning, and error recovery for robotic systems is demonstrated. Our approach to task planning is based on an AND/OR net representation, which is then mapped to a Petri net representation of all feasible geometric states and associated feasibility criteria for net transitions. Task decomposition of robotic assembly plans based on this representation is performed on the Petri net for robotic assembly tasks, and the inheritance of properties of liveness, safeness, and reversibility at all levels of decomposition are explored. This approach provides a framework for robust execution of tasks through the properties of traceability and viability. Uncertainty in robotic systems are modeled by local fuzzy variables, fuzzy marking variables, and global fuzzy variables which are incorporated in fuzzy Petri nets. Analysis of properties and reasoning about uncertainty are investigated using fuzzy reasoning structures built into the net. Two applications of fuzzy Petri nets, robot task sequence planning and sensor-based error recovery, are explored. In the first application, the search space for feasible and complete task sequences with correct precedence relationships is reduced via the use of global fuzzy variables in reasoning about subgoals. In the second application, sensory verification operations are modeled by mutually exclusive transitions to reason about local and global fuzzy variables on-line and automatically select a retry or an alternative error recovery sequence when errors occur. Task sequencing and task execution with error recovery capability for one and multiple soft components in robotic systems are investigated.

Analysis of Phase-Type Stochastic Petri Nets With Discrete and Continuous Timing

NASA Technical Reports Server (NTRS)

Jones, Robert L.; Goode, Plesent W. (Technical Monitor)

2000-01-01

The Petri net formalism is useful in studying many discrete-state, discrete-event systems exhibiting concurrency, synchronization, and other complex behavior. As a bipartite graph, the net can conveniently capture salient aspects of the system. As a mathematical tool, the net can specify an analyzable state space. Indeed, one can reason about certain qualitative properties (from state occupancies) and how they arise (the sequence of events leading there). By introducing deterministic or random delays, the model is forced to sojourn in states some amount of time, giving rise to an underlying stochastic process, one that can be specified in a compact way and capable of providing quantitative, probabilistic measures. We formalize a new non-Markovian extension to the Petri net that captures both discrete and continuous timing in the same model. The approach affords efficient, stationary analysis in most cases and efficient transient analysis under certain restrictions. Moreover, this new formalism has the added benefit in modeling fidelity stemming from the simultaneous capture of discrete- and continuous-time events (as opposed to capturing only one and approximating the other). We show how the underlying stochastic process, which is non-Markovian, can be resolved into simpler Markovian problems that enjoy efficient solutions. Solution algorithms are provided that can be easily programmed.

A Method to Preclude Moisture Condensation in Plated Tissue Cultures

Treesearch

Alex M. Diner

1992-01-01

Excessive condensate normally accumulates in in vitro-illuminated petri dishes containing plant tissue cultures, causing avariety of problems. A dark-colored rubber net-mesh placed over the petri dishes prevented such condensation, even when charcoal-supplemented media are used under high light intensity in a growth chamber.

Suboptimal liveness-enforcing supervisor design for a class of generalised Petri nets using partial siphon enumeration and mathematical programming

NASA Astrophysics Data System (ADS)

Zhao, Mi; Li, ZhiWu; Hu, HeSuan

2010-09-01

This article develops a deadlock prevention policy for a class of generalised Petri nets, which can well model a large class of flexible manufacturing systems. The analysis of such a system leads us to characterise the deadlock situations in terms of the insufficiently marked siphons in its generalised Petri-net model. The proposed policy is carried out in an iterative way. At each step a minimal siphon is derived from a maximal deadly marked siphon that is found by solving a mixed integer programming (MIP) problem. An algorithm is formalised that can efficiently compute such a minimal siphon from a maximal one. A monitor is added for a derived minimal siphon such that it is max-controlled if it is elementary with respect to the siphons that have been derived. The liveness of the controlled system is decided by the fact that no siphon can be derived due to the MIP solution. After a liveness-enforcing net supervisor computed without complete siphon enumeration, the output-arcs of the additional monitors are rearranged such that the monitors act while restricting the system less. Examples are presented to demonstrate the proposed method.

A Petri net synthesis theory for modeling flexible manufacturing systems.

PubMed

Jeng, M D

1997-01-01

A theory that synthesizes Petri nets for modeling flexible manufacturing systems is presented. The theory adopts a bottom-up or modular-composition approach to construct net models. Each module is modeled as a resource control net (RCN), which represents a subsystem that controls a resource type in a flexible manufacturing system. Interactions among the modules are described as the common transition and transition subnets. The net obtained by merging the modules with two minimal restrictions is shown to be conservative and thus bounded. An algorithm is developed to detect two sufficient conditions for structural liveness of the net. The algorithm examines only the net's structure and the initial marking, and appears to be more efficient than state enumeration techniques such as the reachability tree method. In this paper, the sufficient conditions for liveness are shown to be related to some structural objects called siphons. To demonstrate the applicability of the theory, a flexible manufacturing system of a moderate size is modeled and analyzed using the proposed theory.

Petri net-based prediction of therapeutic targets that recover abnormally phosphorylated proteins in muscle atrophy.

PubMed

Jung, Jinmyung; Kwon, Mijin; Bae, Sunghwa; Yim, Soorin; Lee, Doheon

2018-03-05

Muscle atrophy, an involuntary loss of muscle mass, is involved in various diseases and sometimes leads to mortality. However, therapeutics for muscle atrophy thus far have had limited effects. Here, we present a new approach for therapeutic target prediction using Petri net simulation of the status of phosphorylation, with a reasonable assumption that the recovery of abnormally phosphorylated proteins can be a treatment for muscle atrophy. The Petri net model was employed to simulate phosphorylation status in three states, i.e. reference, atrophic and each gene-inhibited state based on the myocyte-specific phosphorylation network. Here, we newly devised a phosphorylation specific Petri net that involves two types of transitions (phosphorylation or de-phosphorylation) and two types of places (activation with or without phosphorylation). Before predicting therapeutic targets, the simulation results in reference and atrophic states were validated by Western blotting experiments detecting five marker proteins, i.e. RELA, SMAD2, SMAD3, FOXO1 and FOXO3. Finally, we determined 37 potential therapeutic targets whose inhibition recovers the phosphorylation status from an atrophic state as indicated by the five validated marker proteins. In the evaluation, we confirmed that the 37 potential targets were enriched for muscle atrophy-related terms such as actin and muscle contraction processes, and they were also significantly overlapping with the genes associated with muscle atrophy reported in the Comparative Toxicogenomics Database (p-value < 0.05). Furthermore, we noticed that they included several proteins that could not be characterized by the shortest path analysis. The three potential targets, i.e. BMPR1B, ROCK, and LEPR, were manually validated with the literature. In this study, we suggest a new approach to predict potential therapeutic targets of muscle atrophy with an analysis of phosphorylation status simulated by Petri net. We generated a list of the potential therapeutic targets whose inhibition recovers abnormally phosphorylated proteins in an atrophic state. They were evaluated by various approaches, such as Western blotting, GO terms, literature, known muscle atrophy-related genes and shortest path analysis. We expect the new proposed strategy to provide an understanding of phosphorylation status in muscle atrophy and to provide assistance towards identifying new therapies.

Executable Architecture Modeling and Simulation Based on fUML

DTIC Science & Technology

2014-06-01

SoS behaviors. Wang et al.[9] use SysML sequence diagram to model the behaviors and translate the models into Colored Petri Nets (CPN). Staines T.S...Renzhong and Dagli C H. An executable system architecture approach to discrete events system modeling using SysML in conjunction with colored Petri

Hybrid modeling in biochemical systems theory by means of functional petri nets.

PubMed

Wu, Jialiang; Voit, Eberhard

2009-02-01

Many biological systems are genuinely hybrids consisting of interacting discrete and continuous components and processes that often operate at different time scales. It is therefore desirable to create modeling frameworks capable of combining differently structured processes and permitting their analysis over multiple time horizons. During the past 40 years, Biochemical Systems Theory (BST) has been a very successful approach to elucidating metabolic, gene regulatory, and signaling systems. However, its foundation in ordinary differential equations has precluded BST from directly addressing problems containing switches, delays, and stochastic effects. In this study, we extend BST to hybrid modeling within the framework of Hybrid Functional Petri Nets (HFPN). First, we show how the canonical GMA and S-system models in BST can be directly implemented in a standard Petri Net framework. In a second step we demonstrate how to account for different types of time delays as well as for discrete, stochastic, and switching effects. Using representative test cases, we validate the hybrid modeling approach through comparative analyses and simulations with other approaches and highlight the feasibility, quality, and efficiency of the hybrid method.

STEPP--Search Tool for Exploration of Petri net Paths: a new tool for Petri net-based path analysis in biochemical networks.

PubMed

Koch, Ina; Schueler, Markus; Heiner, Monika

2005-01-01

To understand biochemical processes caused by, e. g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber.

STEPP - Search Tool for Exploration of Petri net Paths: A New Tool for Petri Net-Based Path Analysis in Biochemical Networks.

PubMed

Koch, Ina; Schüler, Markus; Heiner, Monika

2011-01-01

To understand biochemical processes caused by, e.g., mutations or deletions in the genome, the knowledge of possible alternative paths between two arbitrary chemical compounds is of increasing interest for biotechnology, pharmacology, medicine, and drug design. With the steadily increasing amount of data from high-throughput experiments new biochemical networks can be constructed and existing ones can be extended, which results in many large metabolic, signal transduction, and gene regulatory networks. The search for alternative paths within these complex and large networks can provide a huge amount of solutions, which can not be handled manually. Moreover, not all of the alternative paths are generally of interest. Therefore, we have developed and implemented a method, which allows us to define constraints to reduce the set of all structurally possible paths to the truly interesting path set. The paper describes the search algorithm and the constraints definition language. We give examples for path searches using this dedicated special language for a Petri net model of the sucrose-to-starch breakdown in the potato tuber. http://sanaga.tfh-berlin.de/~stepp/

Utilizing semantic networks to database and retrieve generalized stochastic colored Petri nets

NASA Technical Reports Server (NTRS)

Farah, Jeffrey J.; Kelley, Robert B.

1992-01-01

Previous work has introduced the Planning Coordinator (PCOORD), a coordinator functioning within the hierarchy of the Intelligent Machine Mode. Within the structure of the Planning Coordinator resides the Primitive Structure Database (PSDB) functioning to provide the primitive structures utilized by the Planning Coordinator in the establishing of error recovery or on-line path plans. This report further explores the Primitive Structure Database and establishes the potential of utilizing semantic networks as a means of efficiently storing and retrieving the Generalized Stochastic Colored Petri Nets from which the error recovery plans are derived.

Reliability analysis of repairable systems using Petri nets and vague Lambda-Tau methodology.

PubMed

Garg, Harish

2013-01-01

The main objective of the paper is to developed a methodology, named as vague Lambda-Tau, for reliability analysis of repairable systems. Petri net tool is applied to represent the asynchronous and concurrent processing of the system instead of fault tree analysis. To enhance the relevance of the reliability study, vague set theory is used for representing the failure rate and repair times instead of classical(crisp) or fuzzy set theory because vague sets are characterized by a truth membership function and false membership functions (non-membership functions) so that sum of both values is less than 1. The proposed methodology involves qualitative modeling using PN and quantitative analysis using Lambda-Tau method of solution with the basic events represented by intuitionistic fuzzy numbers of triangular membership functions. Sensitivity analysis has also been performed and the effects on system MTBF are addressed. The methodology improves the shortcomings of the existing probabilistic approaches and gives a better understanding of the system behavior through its graphical representation. The washing unit of a paper mill situated in a northern part of India, producing approximately 200 ton of paper per day, has been considered to demonstrate the proposed approach. The results may be helpful for the plant personnel for analyzing the systems' behavior and to improve their performance by adopting suitable maintenance strategies. Copyright © 2012 ISA. Published by Elsevier Ltd. All rights reserved.

State-based verification of RTCP-nets with nuXmv

NASA Astrophysics Data System (ADS)

Biernacka, Agnieszka; Biernacki, Jerzy; Szpyrka, Marcin

2015-12-01

The paper deals with an algorithm of translation of RTCP-nets' (real-time coloured Petri nets) coverability graphs into nuXmv state machines. The approach enables users to verify RTCP-nets with model checking techniques provided by the nuXmv tool. Full details of the algorithm are presented and an illustrative example of the approach usefulness is provided.

Action-based verification of RTCP-nets with CADP

NASA Astrophysics Data System (ADS)

Biernacki, Jerzy; Biernacka, Agnieszka; Szpyrka, Marcin

2015-12-01

The paper presents an RTCP-nets' (real-time coloured Petri nets) coverability graphs into Aldebaran format translation algorithm. The approach provides the possibility of automatic RTCP-nets verification using model checking techniques provided by the CADP toolbox. An actual fire alarm control panel system has been modelled and several of its crucial properties have been verified to demonstrate the usability of the approach.

On the Use of Kronecker Operators for the Solution of Generalized Stochastic Petri Nets

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Tilgner, Marco

1996-01-01

We discuss how to describe the Markov chain underlying a generalized stochastic Petri net using Kronecker operators on smaller matrices. We extend previous approaches by allowing both an extensive type of marking-dependent behavior for the transitions and the presence of immediate synchronizations. The derivation of the results is thoroughly formalized, including the use of Kronecker operators in the treatment of the vanishing markings and the computation of impulse-based reward measures. We use our techniques to analyze a model whose solution using conventional methods would fail because of the state-space explosion. In the conclusion, we point out ideas to parallelize our approach.

C code generation from Petri-net-based logic controller specification

NASA Astrophysics Data System (ADS)

Grobelny, Michał; Grobelna, Iwona; Karatkevich, Andrei

2017-08-01

The article focuses on programming of logic controllers. It is important that a programming code of a logic controller is executed flawlessly according to the primary specification. In the presented approach we generate C code for an AVR microcontroller from a rule-based logical model of a control process derived from a control interpreted Petri net. The same logical model is also used for formal verification of the specification by means of the model checking technique. The proposed rule-based logical model and formal rules of transformation ensure that the obtained implementation is consistent with the already verified specification. The approach is validated by practical experiments.

A vector matching method for analysing logic Petri nets

NASA Astrophysics Data System (ADS)

Du, YuYue; Qi, Liang; Zhou, MengChu

2011-11-01

Batch processing function and passing value indeterminacy in cooperative systems can be described and analysed by logic Petri nets (LPNs). To directly analyse the properties of LPNs, the concept of transition enabling vector sets is presented and a vector matching method used to judge the enabling transitions is proposed in this article. The incidence matrix of LPNs is defined; an equation about marking change due to a transition's firing is given; and a reachable tree is constructed. The state space explosion is mitigated to a certain extent from directly analysing LPNs. Finally, the validity and reliability of the proposed method are illustrated by an example in electronic commerce.

Methodology for automating software systems

NASA Technical Reports Server (NTRS)

Moseley, Warren

1990-01-01

Applying ITS technology to the shuttle diagnostics would not require the rigor of the Petri Net representation, however it is important in providing the animated simulated portion of the interface and the demands placed on the system to support the training aspects to have a homogeneous and consistent underlying knowledge representation. By keeping the diagnostic rule base, the hardware description, the software description, user profiles, desired behavioral knowledge, and the user interface in the same notation, it is possible to reason about the all of the properties of petri nets, on any selected portion of the simulation. This reasoning provides foundation for utilization of intelligent tutoring systems technology.

A Petri net approach to the study of persistence in chemical reaction networks.

PubMed

Angeli, David; De Leenheer, Patrick; Sontag, Eduardo D

2007-12-01

Persistence is the property, for differential equations in R(n), that solutions starting in the positive orthant do not approach the boundary of the orthant. For chemical reactions and population models, this translates into the non-extinction property: provided that every species is present at the start of the reaction, no species will tend to be eliminated in the course of the reaction. This paper provides checkable conditions for persistence of chemical species in reaction networks, using concepts and tools from Petri net theory, and verifies these conditions on various systems which arise in the modeling of cell signaling pathways.

Modelling the protocol stack in NCS with deterministic and stochastic petri net

NASA Astrophysics Data System (ADS)

Hui, Chen; Chunjie, Zhou; Weifeng, Zhu

2011-06-01

Protocol stack is the basis of the networked control systems (NCS). Full or partial reconfiguration of protocol stack offers both optimised communication service and system performance. Nowadays, field testing is unrealistic to determine the performance of reconfigurable protocol stack; and the Petri net formal description technique offers the best combination of intuitive representation, tool support and analytical capabilities. Traditionally, separation between the different layers of the OSI model has been a common practice. Nevertheless, such a layered modelling analysis framework of protocol stack leads to the lack of global optimisation for protocol reconfiguration. In this article, we proposed a general modelling analysis framework for NCS based on the cross-layer concept, which is to establish an efficiency system scheduling model through abstracting the time constraint, the task interrelation, the processor and the bus sub-models from upper and lower layers (application, data link and physical layer). Cross-layer design can help to overcome the inadequacy of global optimisation based on information sharing between protocol layers. To illustrate the framework, we take controller area network (CAN) as a case study. The simulation results of deterministic and stochastic Petri-net (DSPN) model can help us adjust the message scheduling scheme and obtain better system performance.

Petri Net and Probabilistic Model Checking Based Approach for the Modelling, Simulation and Verification of Internet Worm Propagation

PubMed Central

Razzaq, Misbah; Ahmad, Jamil

2015-01-01

Internet worms are analogous to biological viruses since they can infect a host and have the ability to propagate through a chosen medium. To prevent the spread of a worm or to grasp how to regulate a prevailing worm, compartmental models are commonly used as a means to examine and understand the patterns and mechanisms of a worm spread. However, one of the greatest challenge is to produce methods to verify and validate the behavioural properties of a compartmental model. This is why in this study we suggest a framework based on Petri Nets and Model Checking through which we can meticulously examine and validate these models. We investigate Susceptible-Exposed-Infectious-Recovered (SEIR) model and propose a new model Susceptible-Exposed-Infectious-Recovered-Delayed-Quarantined (Susceptible/Recovered) (SEIDQR(S/I)) along with hybrid quarantine strategy, which is then constructed and analysed using Stochastic Petri Nets and Continuous Time Markov Chain. The analysis shows that the hybrid quarantine strategy is extremely effective in reducing the risk of propagating the worm. Through Model Checking, we gained insight into the functionality of compartmental models. Model Checking results validate simulation ones well, which fully support the proposed framework. PMID:26713449

Petri Net and Probabilistic Model Checking Based Approach for the Modelling, Simulation and Verification of Internet Worm Propagation.

PubMed

Razzaq, Misbah; Ahmad, Jamil

2015-01-01

Internet worms are analogous to biological viruses since they can infect a host and have the ability to propagate through a chosen medium. To prevent the spread of a worm or to grasp how to regulate a prevailing worm, compartmental models are commonly used as a means to examine and understand the patterns and mechanisms of a worm spread. However, one of the greatest challenge is to produce methods to verify and validate the behavioural properties of a compartmental model. This is why in this study we suggest a framework based on Petri Nets and Model Checking through which we can meticulously examine and validate these models. We investigate Susceptible-Exposed-Infectious-Recovered (SEIR) model and propose a new model Susceptible-Exposed-Infectious-Recovered-Delayed-Quarantined (Susceptible/Recovered) (SEIDQR(S/I)) along with hybrid quarantine strategy, which is then constructed and analysed using Stochastic Petri Nets and Continuous Time Markov Chain. The analysis shows that the hybrid quarantine strategy is extremely effective in reducing the risk of propagating the worm. Through Model Checking, we gained insight into the functionality of compartmental models. Model Checking results validate simulation ones well, which fully support the proposed framework.

The signaling petri net-based simulator: a non-parametric strategy for characterizing the dynamics of cell-specific signaling networks.

PubMed

Ruths, Derek; Muller, Melissa; Tseng, Jen-Te; Nakhleh, Luay; Ram, Prahlad T

2008-02-29

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations.

The Signaling Petri Net-Based Simulator: A Non-Parametric Strategy for Characterizing the Dynamics of Cell-Specific Signaling Networks

PubMed Central

Ruths, Derek; Muller, Melissa; Tseng, Jen-Te; Nakhleh, Luay; Ram, Prahlad T.

2008-01-01

Reconstructing cellular signaling networks and understanding how they work are major endeavors in cell biology. The scale and complexity of these networks, however, render their analysis using experimental biology approaches alone very challenging. As a result, computational methods have been developed and combined with experimental biology approaches, producing powerful tools for the analysis of these networks. These computational methods mostly fall on either end of a spectrum of model parameterization. On one end is a class of structural network analysis methods; these typically use the network connectivity alone to generate hypotheses about global properties. On the other end is a class of dynamic network analysis methods; these use, in addition to the connectivity, kinetic parameters of the biochemical reactions to predict the network's dynamic behavior. These predictions provide detailed insights into the properties that determine aspects of the network's structure and behavior. However, the difficulty of obtaining numerical values of kinetic parameters is widely recognized to limit the applicability of this latter class of methods. Several researchers have observed that the connectivity of a network alone can provide significant insights into its dynamics. Motivated by this fundamental observation, we present the signaling Petri net, a non-parametric model of cellular signaling networks, and the signaling Petri net-based simulator, a Petri net execution strategy for characterizing the dynamics of signal flow through a signaling network using token distribution and sampling. The result is a very fast method, which can analyze large-scale networks, and provide insights into the trends of molecules' activity-levels in response to an external stimulus, based solely on the network's connectivity. We have implemented the signaling Petri net-based simulator in the PathwayOracle toolkit, which is publicly available at http://bioinfo.cs.rice.edu/pathwayoracle. Using this method, we studied a MAPK1,2 and AKT signaling network downstream from EGFR in two breast tumor cell lines. We analyzed, both experimentally and computationally, the activity level of several molecules in response to a targeted manipulation of TSC2 and mTOR-Raptor. The results from our method agreed with experimental results in greater than 90% of the cases considered, and in those where they did not agree, our approach provided valuable insights into discrepancies between known network connectivities and experimental observations. PMID:18463702

Classical workflow nets and workflow nets with reset arcs: using Lyapunov stability for soundness verification

NASA Astrophysics Data System (ADS)

Clempner, Julio B.

2017-01-01

This paper presents a novel analytical method for soundness verification of workflow nets and reset workflow nets, using the well-known stability results of Lyapunov for Petri nets. We also prove that the soundness property is decidable for workflow nets and reset workflow nets. In addition, we provide evidence of several outcomes related with properties such as boundedness, liveness, reversibility and blocking using stability. Our approach is validated theoretically and by a numerical example related to traffic signal-control synchronisation.

Petri net modeling of encrypted information flow in federated cloud

NASA Astrophysics Data System (ADS)

Khushk, Abdul Rauf; Li, Xiaozhong

2017-08-01

Solutions proposed and developed for the cost-effective cloud systems suffer from a combination of secure private clouds and less secure public clouds. Need to locate applications within different clouds poses a security risk to the information flow of the entire system. This study addresses this by assigning security levels of a given lattice to the entities of a federated cloud system. A dynamic flow sensitive security model featuring Bell-LaPadula procedures is explored that tracks and authenticates the secure information flow in federated clouds. Additionally, a Petri net model is considered as a case study to represent the proposed system and further validate the performance of the said system.

The use of the Petri net method in the simulation modeling of mitochondrial swelling.

PubMed

Danylovych, Yu V; Chunikhin, A Y; Danylovych, G V; Kolomiets, O V

2016-01-01

Using photon correlation spectroscopy, which allows investigating changes in the hydrodynamic dia­meter of the particles in suspension, it was shown that ultrahigh concentrations of Ca2+ (over 10 mM) induce swelling of isolated mitochondria. An increase in hydrodynamic diameter was caused by an increase of non-specific mitochondrial membrane permeability to Ca ions, matrix Ca2+ overload, activation of ATP- and Ca2+-sensitive K+-channels, as well as activation of cyclosporin-sensitive permeability transition pore. To formalize the experimental data and to assess conformity of experimental results with theoretical predictions we developed a simulation model using the hybrid functional Petri net method.

Development of petri net-based dynamic model for improved production of farnesyl pyrophosphate by integrating mevalonate and methylerythritol phosphate pathways in yeast.

PubMed

Baadhe, Rama Raju; Mekala, Naveen Kumar; Palagiri, Satwik Reddy; Parcha, Sreenivasa Rao

2012-07-01

In this case study, we designed a farnesyl pyrophosphate (FPP) biosynthetic network using hybrid functional Petri net with extension (HFPNe) which is derived from traditional Petri net theory and allows easy modeling with graphical approach of various types of entities in the networks together. Our main objective is to improve the production of FPP in yeast, which is further converted to amorphadiene (AD), a precursor of artemisinin (antimalarial drug). Natively, mevalonate (MEV) pathway is present in yeast. Methyl erythritol phosphate pathways (MEP) are present only in higher plant plastids and eubacteria, but not present in yeast. IPP and DAMP are common isomeric intermediate in these two pathways, which immediately yields FPP. By integrating these two pathways in yeast, we augmented the FPP synthesis approximately two folds higher (431.16 U/pt) than in MEV pathway alone (259.91 U/pt) by using HFPNe technique. Further enhanced FPP levels converted to AD by amorphadiene synthase gene yielding 436.5 U/pt of AD which approximately two folds higher compared to the AD (258.5 U/pt) synthesized by MEV pathway exclusively. Simulation and validation processes performed using these models are reliable with identified biological information and data.

Deciding the liveness for a subclass of weighted Petri nets based on structurally circular wait

NASA Astrophysics Data System (ADS)

Liu, GuanJun; Chen, LiJing

2016-05-01

Weighted Petri nets as a kind of formal language are widely used to model and verify discrete event systems related to resource allocation like flexible manufacturing systems. System of Simple Sequential Processes with Multi-Resources (S3PMR, a subclass of weighted Petri nets and an important extension to the well-known System of Simple Sequential Processes with Resources, can model many discrete event systems in which (1) multiple processes may run in parallel and (2) each execution step of each process may use multiple units from multiple resource types. This paper gives a necessary and sufficient condition for the liveness of S3PMR. A new structural concept called Structurally Circular Wait (SCW) is proposed for S3PMR. Blocking Marking (BM) associated with an SCW is defined. It is proven that a marked S3PMR is live if and only if each SCW has no BM. We use an example of multi-processor system-on-chip to show that SCW and BM can precisely characterise the (partial) deadlocks for S3PMR. Simultaneously, two examples are used to show the advantages of SCW in preventing deadlocks of S3PMR. These results are significant for the further research on dealing with the deadlock problem.

Application of Petri net based analysis techniques to signal transduction pathways.

PubMed

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-11-02

Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules.

Application of Petri net based analysis techniques to signal transduction pathways

PubMed Central

Sackmann, Andrea; Heiner, Monika; Koch, Ina

2006-01-01

Background Signal transduction pathways are usually modelled using classical quantitative methods, which are based on ordinary differential equations (ODEs). However, some difficulties are inherent in this approach. On the one hand, the kinetic parameters involved are often unknown and have to be estimated. With increasing size and complexity of signal transduction pathways, the estimation of missing kinetic data is not possible. On the other hand, ODEs based models do not support any explicit insights into possible (signal-) flows within the network. Moreover, a huge amount of qualitative data is available due to high-throughput techniques. In order to get information on the systems behaviour, qualitative analysis techniques have been developed. Applications of the known qualitative analysis methods concern mainly metabolic networks. Petri net theory provides a variety of established analysis techniques, which are also applicable to signal transduction models. In this context special properties have to be considered and new dedicated techniques have to be designed. Methods We apply Petri net theory to model and analyse signal transduction pathways first qualitatively before continuing with quantitative analyses. This paper demonstrates how to build systematically a discrete model, which reflects provably the qualitative biological behaviour without any knowledge of kinetic parameters. The mating pheromone response pathway in Saccharomyces cerevisiae serves as case study. Results We propose an approach for model validation of signal transduction pathways based on the network structure only. For this purpose, we introduce the new notion of feasible t-invariants, which represent minimal self-contained subnets being active under a given input situation. Each of these subnets stands for a signal flow in the system. We define maximal common transition sets (MCT-sets), which can be used for t-invariant examination and net decomposition into smallest biologically meaningful functional units. Conclusion The paper demonstrates how Petri net analysis techniques can promote a deeper understanding of signal transduction pathways. The new concepts of feasible t-invariants and MCT-sets have been proven to be useful for model validation and the interpretation of the biological system behaviour. Whereas MCT-sets provide a decomposition of the net into disjunctive subnets, feasible t-invariants describe subnets, which generally overlap. This work contributes to qualitative modelling and to the analysis of large biological networks by their fully automatic decomposition into biologically meaningful modules. PMID:17081284

A PetriNet-Based Approach for Supporting Traceability in Cyber-Physical Manufacturing Systems

PubMed Central

Huang, Jiwei; Zhu, Yeping; Cheng, Bo; Lin, Chuang; Chen, Junliang

2016-01-01

With the growing popularity of complex dynamic activities in manufacturing processes, traceability of the entire life of every product has drawn significant attention especially for food, clinical materials, and similar items. This paper studies the traceability issue in cyber-physical manufacturing systems from a theoretical viewpoint. Petri net models are generalized for formulating dynamic manufacturing processes, based on which a detailed approach for enabling traceability analysis is presented. Models as well as algorithms are carefully designed, which can trace back the lifecycle of a possibly contaminated item. A practical prototype system for supporting traceability is designed, and a real-life case study of a quality control system for bee products is presented to validate the effectiveness of the approach. PMID:26999141

New insights into the human body iron metabolism analyzed by a Petri net based approach.

PubMed

Sackmann, Andrea; Formanowicz, Dorota; Formanowicz, Piotr; Blazewicz, Jacek

2009-04-01

Iron homeostasis is one of the most important biochemical processes in the human body. Despite this fact, the process is not fully understood and until recently only rough descriptions of parts of the process could be found in the literature. Here, an extension of the recently published formal model of the main part of the process is presented. This extension consists in including all known mechanisms of hepcidin regulation. Hepcidin is a hormone synthesized in the liver which is mainly responsible for an inhibition of iron absorption in the small intestine during an inflammatory process. The model is expressed in the language of Petri net theory which allows for its relatively easy analysis and simulation.

A PetriNet-Based Approach for Supporting Traceability in Cyber-Physical Manufacturing Systems.

PubMed

Huang, Jiwei; Zhu, Yeping; Cheng, Bo; Lin, Chuang; Chen, Junliang

2016-03-17

With the growing popularity of complex dynamic activities in manufacturing processes, traceability of the entire life of every product has drawn significant attention especially for food, clinical materials, and similar items. This paper studies the traceability issue in cyber-physical manufacturing systems from a theoretical viewpoint. Petri net models are generalized for formulating dynamic manufacturing processes, based on which a detailed approach for enabling traceability analysis is presented. Models as well as algorithms are carefully designed, which can trace back the lifecycle of a possibly contaminated item. A practical prototype system for supporting traceability is designed, and a real-life case study of a quality control system for bee products is presented to validate the effectiveness of the approach.

How to Construct an Automated Warehouse Based on Colored Timed Petri Nets

NASA Astrophysics Data System (ADS)

Cheng, Fei; He, Shanjun

The automated warehouse considered here consists of a number of rack locations with three cranes, a narrow aisle shuttle, and several buffer stations with the roller. Based on analyzing of the behaviors of the active resources in the system, a modular and computerized model is presented via a colored timed Petri net approach, in which places are multicolored to simplify model and characterize control flow of the resources, and token colors are defined as the routes of storage/retrieval operations. In addition, an approach for realization of model via visual c++ is briefly given. These facts allow us to render an emulate system to simulate a discrete control application for online monitoring, dynamic dispatching control and off-line revising scheduler policies.

A Petri Net model for distributed energy system

NASA Astrophysics Data System (ADS)

Konopko, Joanna

2015-12-01

Electrical networks need to evolve to become more intelligent, more flexible and less costly. The smart grid is the next generation power energy, uses two-way flows of electricity and information to create a distributed automated energy delivery network. Building a comprehensive smart grid is a challenge for system protection, optimization and energy efficient. Proper modeling and analysis is needed to build an extensive distributed energy system and intelligent electricity infrastructure. In this paper, the whole model of smart grid have been proposed using Generalized Stochastic Petri Nets (GSPN). The simulation of created model is also explored. The simulation of the model has allowed the analysis of how close the behavior of the model is to the usage of the real smart grid.

Materials Research of Novel Organic Piezoelectric/Ferroelectric Compounds at a H.S.I

DTIC Science & Technology

2015-07-06

analysis 4. http://wavefun.com 5. MOPAC2012, James J. P. Stewart, Stewart Computational Chemistry, Colorado Springs, CO, USA, HTTP://OpenMOPAC. net ... petri dish of mineral oil (to prevent electrical arcing) ripples in the mineral oil are clearly visible when a voltage is applied to the sample. We...acid. It does not appear to be ferroelectric. However, it is piezoelectric. When placed in a petri dish of mineral oil (to prevent electrical arcing

A Novel Petri Nets-Based Modeling Method for the Interaction between the Sensor and the Geographic Environment in Emerging Sensor Networks

PubMed Central

Zhang, Feng; Xu, Yuetong; Chou, Jarong

2016-01-01

The service of sensor device in Emerging Sensor Networks (ESNs) is the extension of traditional Web services. Through the sensor network, the service of sensor device can communicate directly with the entity in the geographic environment, and even impact the geographic entity directly. The interaction between the sensor device in ESNs and geographic environment is very complex, and the interaction modeling is a challenging problem. This paper proposed a novel Petri Nets-based modeling method for the interaction between the sensor device and the geographic environment. The feature of the sensor device service in ESNs is more easily affected by the geographic environment than the traditional Web service. Therefore, the response time, the fault-tolerant ability and the resource consumption become important factors in the performance of the whole sensor application system. Thus, this paper classified IoT services as Sensing services and Controlling services according to the interaction between IoT service and geographic entity, and classified GIS services as data services and processing services. Then, this paper designed and analyzed service algebra and Colored Petri Nets model to modeling the geo-feature, IoT service, GIS service and the interaction process between the sensor and the geographic enviroment. At last, the modeling process is discussed by examples. PMID:27681730

Specification and Verification of Medical Monitoring System Using Petri-nets.

PubMed

Majma, Negar; Babamir, Seyed Morteza

2014-07-01

To monitor the patient behavior, data are collected from patient's body by a medical monitoring device so as to calculate the output using embedded software. Incorrect calculations may endanger the patient's life if the software fails to meet the patient's requirements. Accordingly, the veracity of the software behavior is a matter of concern in the medicine; moreover, the data collected from the patient's body are fuzzy. Some methods have already dealt with monitoring the medical monitoring devices; however, model based monitoring fuzzy computations of such devices have been addressed less. The present paper aims to present synthesizing a fuzzy Petri-net (FPN) model to verify behavior of a sample medical monitoring device called continuous infusion insulin (INS) because Petri-net (PN) is one of the formal and visual methods to verify the software's behavior. The device is worn by the diabetic patients and then the software calculates the INS dose and makes a decision for injection. The input and output of the infusion INS software are not crisp in the real world; therefore, we present them in fuzzy variables. Afterwards, we use FPN instead of clear PN to model the fuzzy variables. The paper follows three steps to synthesize an FPN to deal with verification of the infusion INS device: (1) Definition of fuzzy variables, (2) definition of fuzzy rules and (3) design of the FPN model to verify the software behavior.

Petri net siphon analysis and graph theoretic measures for identifying combination therapies in cancer.

PubMed

Behinaein, Behnam; Rudie, Karen; Sangrar, Waheed

2016-10-03

Epidermal Growth Factor Receptor (EGFR) signaling to the Ras-MAPK pathway is implicated in the development and progression of cancer and is a major focus of targeted combination therapies. Physiochemical models have been used for identifying and testing the signal-inhibiting potential of targeted therapies, however, their application to larger multi-pathway networks is limited by the availability of experimentally-determined rate and concentration parameters. An alternate strategy for identifying and evaluating drug-targetable nodes is proposed. A physiochemical model of EGFR-Ras-MAPK signaling is implemented and calibrated to experimental data. Essential topological features of the model are converted into a Petri net and nodes that behave as siphons-a structural property of Petri nets-are identified. Siphons represent potential drug-targets since they are unrecoverable if their values fall below a threshold. Centrality measures are then used to prioritize siphons identified as candidate drug-targets. Single and multiple drug-target combinations are identified which correspond to clinically relevant drug targets and exhibit inhibition synergy in physiochemical simulations of EGF-induced EGFR-Ras-MAPK signaling. Taken together, these studies suggest that siphons and centrality analyses are a promising computational strategy to identify and rank drug-targetable nodes in larger networks as they do not require knowledge of the dynamics of the system, but rely solely on topology.

Colored petri net modeling of small interfering RNA-mediated messenger RNA degradation.

PubMed

Nickaeen, Niloofar; Moein, Shiva; Heidary, Zarifeh; Ghaisari, Jafar

2016-01-01

Mathematical modeling of biological systems is an attractive way for studying complex biological systems and their behaviors. Petri Nets, due to their ability to model systems with various levels of qualitative information, have been wildly used in modeling biological systems in which enough qualitative data may not be at disposal. These nets have been used to answer questions regarding the dynamics of different cell behaviors including the translation process. In one stage of the translation process, the RNA sequence may be degraded. In the process of degradation of RNA sequence, small-noncoding RNA molecules known as small interfering RNA (siRNA) match the target RNA sequence. As a result of this matching, the target RNA sequence is destroyed. In this context, the process of matching and destruction is modeled using Colored Petri Nets (CPNs). The model is constructed using CPNs which allow tokens to have a value or type on them. Thus, CPN is a suitable tool to model string structures in which each element of the string has a different type. Using CPNs, long RNA, and siRNA strings are modeled with a finite set of colors. The model is simulated via CPN Tools. A CPN model of the matching between RNA and siRNA strings is constructed in CPN Tools environment. In previous studies, a network of stoichiometric equations was modeled. However, in this particular study, we modeled the mechanism behind the silencing process. Modeling this kind of mechanisms provides us with a tool to examine the effects of different factors such as mutation or drugs on the process.

A Binary Array Asynchronous Sorting Algorithm with Using Petri Nets

NASA Astrophysics Data System (ADS)

Voevoda, A. A.; Romannikov, D. O.

2017-01-01

Nowadays the tasks of computations speed-up and/or their optimization are actual. Among the approaches on how to solve these tasks, a method applying approaches of parallelization and asynchronization to a sorting algorithm is considered in the paper. The sorting methods are ones of elementary methods and they are used in a huge amount of different applications. In the paper, we offer a method of an array sorting that based on a division into a set of independent adjacent pairs of numbers and their parallel and asynchronous comparison. And this one distinguishes the offered method from the traditional sorting algorithms (like quick sorting, merge sorting, insertion sorting and others). The algorithm is implemented with the use of Petri nets, like the most suitable tool for an asynchronous systems description.

A Petri Net model for distributed energy system

DOE Office of Scientific and Technical Information (OSTI.GOV)

Konopko, Joanna

2015-12-31

Electrical networks need to evolve to become more intelligent, more flexible and less costly. The smart grid is the next generation power energy, uses two-way flows of electricity and information to create a distributed automated energy delivery network. Building a comprehensive smart grid is a challenge for system protection, optimization and energy efficient. Proper modeling and analysis is needed to build an extensive distributed energy system and intelligent electricity infrastructure. In this paper, the whole model of smart grid have been proposed using Generalized Stochastic Petri Nets (GSPN). The simulation of created model is also explored. The simulation of themore » model has allowed the analysis of how close the behavior of the model is to the usage of the real smart grid.« less

Safety analysis of discrete event systems using a simplified Petri net controller.

PubMed

Zareiee, Meysam; Dideban, Abbas; Asghar Orouji, Ali

2014-01-01

This paper deals with the problem of forbidden states in discrete event systems based on Petri net models. So, a method is presented to prevent the system from entering these states by constructing a small number of generalized mutual exclusion constraints. This goal is achieved by solving three types of Integer Linear Programming problems. The problems are designed to verify the constraints that some of them are related to verifying authorized states and the others are related to avoiding forbidden states. The obtained constraints can be enforced on the system using a small number of control places. Moreover, the number of arcs related to these places is small, and the controller after connecting them is maximally permissive. © 2013 ISA. Published by Elsevier Ltd. All rights reserved.

Modeling shared resources with generalized synchronization within a Petri net bottom-up approach.

PubMed

Ferrarini, L; Trioni, M

1996-01-01

This paper proposes a simple and effective way to represent shared resources in manufacturing systems within a Petri net model previously developed. Such a model relies on the bottom-up and modular approach to synthesis and analysis. The designer may define elementary tasks and then connect them with one another with three kinds of connections: self-loops, inhibitor arcs and simple synchronizations. A theoretical framework has been established for the analysis of liveness and reversibility of such models. The generalized synchronization, here formalized, represents an extension of the simple synchronization, allowing the merging of suitable subnets among elementary tasks. It is proved that under suitable, but not restrictive, hypotheses the generalized synchronization may be substituted for a simple one, thus being compatible with all the developed theoretical body.

A proposal of an architecture for the coordination level of intelligent machines

NASA Technical Reports Server (NTRS)

Beard, Randall; Farah, Jeff; Lima, Pedro

1993-01-01

The issue of obtaining a practical, structured, and detailed description of an architecture for the Coordination Level of Center for Intelligent Robotic Systems for Sapce Exploration (CIRSSE) Testbed Intelligent Controller is addressed. Previous theoretical and implementation works were the departure point for the discussion. The document is organized as follows: after this introductory section, section 2 summarizes the overall view of the Intelligent Machine (IM) as a control system, proposing a performance measure on which to base its design. Section 3 addresses with some detail implementation issues. An hierarchic petri-net with feedback-based learning capabilities is proposed. Finally, section 4 is an attempt to address the feedback problem. Feedback is used for two functions: error recovery and reinforcement learning of the correct translations for the petri-net transitions.

Coverability graphs for a class of synchronously executed unbounded Petri net

NASA Technical Reports Server (NTRS)

Stotts, P. David; Pratt, Terrence W.

1990-01-01

After detailing a variant of the concurrent-execution rule for firing of maximal subsets, in which the simultaneous firing of conflicting transitions is prohibited, an algorithm is constructed for generating the coverability graph of a net executed under this synchronous firing rule. The omega insertion criteria in the algorithm are shown to be valid for any net on which the algorithm terminates. It is accordingly shown that the set of nets on which the algorithm terminates includes the 'conflict-free' class.

Modeling and control of operator functional state in a unified framework of fuzzy inference petri nets.

PubMed

Zhang, Jian-Hua; Xia, Jia-Jun; Garibaldi, Jonathan M; Groumpos, Petros P; Wang, Ru-Bin

2017-06-01

In human-machine (HM) hybrid control systems, human operator and machine cooperate to achieve the control objectives. To enhance the overall HM system performance, the discrete manual control task-load by the operator must be dynamically allocated in accordance with continuous-time fluctuation of psychophysiological functional status of the operator, so-called operator functional state (OFS). The behavior of the HM system is hybrid in nature due to the co-existence of discrete task-load (control) variable and continuous operator performance (system output) variable. Petri net is an effective tool for modeling discrete event systems, but for hybrid system involving discrete dynamics, generally Petri net model has to be extended. Instead of using different tools to represent continuous and discrete components of a hybrid system, this paper proposed a method of fuzzy inference Petri nets (FIPN) to represent the HM hybrid system comprising a Mamdani-type fuzzy model of OFS and a logical switching controller in a unified framework, in which the task-load level is dynamically reallocated between the operator and machine based on the model-predicted OFS. Furthermore, this paper used a multi-model approach to predict the operator performance based on three electroencephalographic (EEG) input variables (features) via the Wang-Mendel (WM) fuzzy modeling method. The membership function parameters of fuzzy OFS model for each experimental participant were optimized using artificial bee colony (ABC) evolutionary algorithm. Three performance indices, RMSE, MRE, and EPR, were computed to evaluate the overall modeling accuracy. Experiment data from six participants are analyzed. The results show that the proposed method (FIPN with adaptive task allocation) yields lower breakdown rate (from 14.8% to 3.27%) and higher human performance (from 90.30% to 91.99%). The simulation results of the FIPN-based adaptive HM (AHM) system on six experimental participants demonstrate that the FIPN framework provides an effective way to model and regulate/optimize the OFS in HM hybrid systems composed of continuous-time OFS model and discrete-event switching controller. Copyright © 2017 Elsevier B.V. All rights reserved.

Stochastic Petri Net Modeling of Hypoxia Pathway Predicts a Novel Incoherent Feed-Forward Loop Controlling SDF-1 Expression in Acute Kidney Injury.

PubMed

Heidary, Zarifeh; Ghaisari, Jafar; Moein, Shiva; Naderi, Mahmood; Gheisari, Yousof

2016-01-01

Homing of stem cells to the sites of injury is crucial for tissue regeneration. Stromal derived factor 1 (SDF-1) is among the most important chemokines recruiting these cells. Unexpectedly, our previous experimental data on mouse models of acute kidney injury showed that SDF-1 has a declining trend following ischemic kidney insult. To describe this unforeseen observation, a stochastic Petri net model of SDF-1 regulation in the hypoxia pathway was constructed based on main related components extracted from literature. Using this strategy, predictions regarding the underlying mechanisms of SDF-1 kinetics are generated and a novel incoherent feed forward loop regulating SDF-1 expression is proposed. The computational approach suggested here can be exploited to propose novel therapies for debilitating disorders such as kidney injury.

Using Petri nets for experimental design in a multi-organ elimination pathway.

PubMed

Reshetova, Polina; Smilde, Age K; Westerhuis, Johan A; van Kampen, Antoine H C

2015-08-01

Genistein is a soy metabolite with estrogenic activity that may result in (un)favorable effects on human health. Elucidation of the mechanisms through which food additives such as genistein exert their beneficiary effects is a major challenge for the food industry. A better understanding of the genistein elimination pathway could shed light on such mechanisms. We developed a Petri net model that represents this multi-organ elimination pathway and which assists in the design of future experiments. Using this model we show that metabolic profiles solely measured in venous blood are not sufficient to uniquely parameterize the model. Based on simulations we suggest two solutions that provide better results: parameterize the model using gut epithelium profiles or add additional biological constrains in the model. Copyright © 2015 Elsevier Ltd. All rights reserved.

Improving the Quality of Alerts and Predicting Intruder's Next Goal with Hidden Colored Petri-Net

DOE Office of Scientific and Technical Information (OSTI.GOV)

Yu, Dong; Frincke, Deb A.

2006-06-22

Intrusion detection systems (IDS) often provide poor quality alerts, which are insufficient to support rapid identification of ongoing attacks or predict an intruder’s next likely goal. In this paper, we propose a novel approach to alert post-processing and correlation, the Hidden Colored Petri-Net (HCPN). Different from most other alert correlation methods, our approach treats the alert correlation problem as an inference problem rather than a filter problem. Our approach assumes that the intruder’s actions are unknown to the IDS and can be inferred only from the alerts generated by the IDS sensors. HCPN can describe the relationship between different stepsmore » carried out by intruders, model observations (alerts) and transitions (actions) separately, and associate each token element (system state) with a probability (or confidence). The model is an extension to Colored Petri-Net (CPN) .It is so called “hidden” because the transitions (actions) are not directly observable but can be inferred by looking through the observations (alerts). These features make HCPN especially suitable for discovering intruders’ actions from their partial observations (alerts,) and predicting intruders’ next goal. Our experiments on DARPA evaluation datasets and the attack scenarios from the Grand Challenge Problem (GCP) show that HCPN has promise as a way to reducing false positives and negatives, predicting intruder’s next possible action, uncovering intruders’ intrusion strategies after the attack scenario has happened, and providing confidence scores.« less

Performance and state-space analyses of systems using Petri nets

NASA Technical Reports Server (NTRS)

Watson, James Francis, III

1992-01-01

The goal of any modeling methodology is to develop a mathematical description of a system that is accurate in its representation and also permits analysis of structural and/or performance properties. Inherently, trade-offs exist between the level detail in the model and the ease with which analysis can be performed. Petri nets (PN's), a highly graphical modeling methodology for Discrete Event Dynamic Systems, permit representation of shared resources, finite capacities, conflict, synchronization, concurrency, and timing between state changes. By restricting the state transition time delays to the family of exponential density functions, Markov chain analysis of performance problems is possible. One major drawback of PN's is the tendency for the state-space to grow rapidly (exponential complexity) compared to increases in the PN constructs. It is the state space, or the Markov chain obtained from it, that is needed in the solution of many problems. The theory of state-space size estimation for PN's is introduced. The problem of state-space size estimation is defined, its complexities are examined, and estimation algorithms are developed. Both top-down and bottom-up approaches are pursued, and the advantages and disadvantages of each are described. Additionally, the author's research in non-exponential transition modeling for PN's is discussed. An algorithm for approximating non-exponential transitions is developed. Since only basic PN constructs are used in the approximation, theory already developed for PN's remains applicable. Comparison to results from entropy theory show the transition performance is close to the theoretic optimum. Inclusion of non-exponential transition approximations improves performance results at the expense of increased state-space size. The state-space size estimation theory provides insight and algorithms for evaluating this trade-off.

Command and Control for Large-Scale Hybrid Warfare Systems

DTIC Science & Technology

2014-06-05

Prescribed by ANSI Std Z39-18 2 CK Pang et al. in C2 architectures was proposed using Petri nets (PNs).10 Liao in [11] reported an architecture for...arises from the chal- lenging and often-conflicting user requirements, scale, scope, inter-connectivity with different large-scale net - worked teams and...resources can be easily modelled and reconfigured by the notion of block matrix. At any time, the various missions of the net - worked team can be added

Connecting the dots between genes, biochemistry, and disease susceptibility: systems biology modeling in human genetics.

PubMed

Moore, Jason H; Boczko, Erik M; Summar, Marshall L

2005-02-01

Understanding how DNA sequence variations impact human health through a hierarchy of biochemical and physiological systems is expected to improve the diagnosis, prevention, and treatment of common, complex human diseases. We have previously developed a hierarchical dynamic systems approach based on Petri nets for generating biochemical network models that are consistent with genetic models of disease susceptibility. This modeling approach uses an evolutionary computation approach called grammatical evolution as a search strategy for optimal Petri net models. We have previously demonstrated that this approach routinely identifies biochemical network models that are consistent with a variety of genetic models in which disease susceptibility is determined by nonlinear interactions between two or more DNA sequence variations. We review here this approach and then discuss how it can be used to model biochemical and metabolic data in the context of genetic studies of human disease susceptibility.

Cell illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2011-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Transactions in domain-specific information systems

NASA Astrophysics Data System (ADS)

Zacek, Jaroslav

2017-07-01

Substantial number of the current information system (IS) implementations is based on transaction approach. In addition, most of the implementations are domain-specific (e.g. accounting IS, resource planning IS). Therefore, we have to have a generic transaction model to build and verify domain-specific IS. The paper proposes a new transaction model for domain-specific ontologies. This model is based on value oriented business process modelling technique. The transaction model is formalized by the Petri Net theory. First part of the paper presents common business processes and analyses related to business process modeling. Second part defines the transactional model delimited by REA enterprise ontology paradigm and introduces states of the generic transaction model. The generic model proposal is defined and visualized by the Petri Net modelling tool. Third part shows application of the generic transaction model. Last part of the paper concludes results and discusses a practical usability of the generic transaction model.

A Fuzzy Reasoning Design for Fault Detection and Diagnosis of a Computer-Controlled System

PubMed Central

Ting, Y.; Lu, W.B.; Chen, C.H.; Wang, G.K.

2008-01-01

A Fuzzy Reasoning and Verification Petri Nets (FRVPNs) model is established for an error detection and diagnosis mechanism (EDDM) applied to a complex fault-tolerant PC-controlled system. The inference accuracy can be improved through the hierarchical design of a two-level fuzzy rule decision tree (FRDT) and a Petri nets (PNs) technique to transform the fuzzy rule into the FRVPNs model. Several simulation examples of the assumed failure events were carried out by using the FRVPNs and the Mamdani fuzzy method with MATLAB tools. The reasoning performance of the developed FRVPNs was verified by comparing the inference outcome to that of the Mamdani method. Both methods result in the same conclusions. Thus, the present study demonstratrates that the proposed FRVPNs model is able to achieve the purpose of reasoning, and furthermore, determining of the failure event of the monitored application program. PMID:19255619

A Concurrent Multiple Negotiation Protocol Based on Colored Petri Nets.

PubMed

Niu, Lei; Ren, Fenghui; Zhang, Minjie; Bai, Quan

2017-11-01

Concurrent multiple negotiation (CMN) provides a mechanism for an agent to simultaneously conduct more than one negotiation. There may exist different interdependency relationships among these negotiations and these interdependency relationships can impact the outcomes of these negotiations. The outcomes of these concurrent negotiations contribute together for the agent to achieve an overall negotiation goal. Handling a CMN while considering interdependency relationships among multiple negotiations is a challenging research problem. This paper: 1) comprehensively highlights research problems of negotiations at concurrent negotiation level; 2) provides a graph-based CMN model with consideration of the interdependency relationships; and 3) proposes a colored Petri net-based negotiation protocol for conducting CMNs. With the proposed protocol, a CMN can be efficiently and concurrently processed and negotiation agreements can be efficiently achieved. Experimental results indicate the effectiveness and efficiency of the proposed protocol in terms of the negotiation success rate, the negotiation time and the negotiation outcome.

Stochastic Petri net analysis of a replicated file system

NASA Technical Reports Server (NTRS)

Bechta Dugan, Joanne; Ciardo, Gianfranco

1989-01-01

A stochastic Petri-net model of a replicated file system is presented for a distributed environment where replicated files reside on different hosts and a voting algorithm is used to maintain consistency. Witnesses, which simply record the status of the file but contain no data, can be used in addition to or in place of files to reduce overhead. A model sufficiently detailed to include file status (current or out-of-date), as well as failure and repair of hosts where copies or witnesses reside, is presented. The number of copies and witnesses is a parameter of the model. Two different majority protocols are examined, one where a majority of all copies and witnesses is necessary to form a quorum, and the other where only a majority of the copies and witnesses on operational hosts is needed. The latter, known as adaptive voting, is shown to increase file availability in most cases.

Structural analysis of a Petri net model of oxidative stress in atherosclerosis.

PubMed

Kozak, Adam; Formanowicz, Dorota; Formanowicz, Piotr

2018-06-01

Atherosclerosis is a complex process of gathering sub-endothelial plaques decreasing lumen of the blood vessels. This disorder affects people of all ages, but its progression is asymptomatic for many years. It is regulated by many typical and atypical factors including the immune system response, a chronic kidney disease, a diet rich in lipids, a local inflammatory process and a local oxidative stress that is here one of the key factors. In this study, a Petri net model of atherosclerosis regulation is presented. This model includes also some information about stoichiometric relationships between its components and covers all mentioned factors. For the model, a structural analysis based on invariants was made and biological conclusions are presented. Since the model contains inhibitor arcs, a heuristic method for analysis of such cases is presented. This method can be used to extend the concept of feasible t -invariants.

Stochastic Petri Net extension of a yeast cell cycle model.

PubMed

Mura, Ivan; Csikász-Nagy, Attila

2008-10-21

This paper presents the definition, solution and validation of a stochastic model of the budding yeast cell cycle, based on Stochastic Petri Nets (SPN). A specific family of SPNs is selected for building a stochastic version of a well-established deterministic model. We describe the procedure followed in defining the SPN model from the deterministic ODE model, a procedure that can be largely automated. The validation of the SPN model is conducted with respect to both the results provided by the deterministic one and the experimental results available from literature. The SPN model catches the behavior of the wild type budding yeast cells and a variety of mutants. We show that the stochastic model matches some characteristics of budding yeast cells that cannot be found with the deterministic model. The SPN model fine-tunes the simulation results, enriching the breadth and the quality of its outcome.

Supervisory control based on minimal cuts and Petri net sub-controllers coordination

NASA Astrophysics Data System (ADS)

Rezig, Sadok; Achour, Zied; Rezg, Nidhal; Kammoun, Mohamed-Ali

2016-10-01

This paper addresses the synthesis of Petri net (PN) controller for the forbidden state transition problem with a new utilisation of the theory of regions. Moreover, as any method of control synthesis based on a reachability graph, the theory of regions suffers from the combinatorial explosion problem. The proposed work minimises the number of equations in the linear system of theory of regions and therefore one can reduce the computation time. In this paper, two different approaches are proposed to select minimal cuts in the reachability graph in order to synthesise a PN controller. Thanks to a switch from one cut to another, one can activate and deactivate the corresponding PNcontroller. An application is implemented in a flexible manufacturing system to illustrate the present method. Finally, comparison with previous works with experimental results in obtaining a maximally permissive controller is presented.

Petri-net-based 2D design of DNA walker circuits.

PubMed

Gilbert, David; Heiner, Monika; Rohr, Christian

2018-01-01

We consider localised DNA computation, where a DNA strand walks along a binary decision graph to compute a binary function. One of the challenges for the design of reliable walker circuits consists in leakage transitions, which occur when a walker jumps into another branch of the decision graph. We automatically identify leakage transitions, which allows for a detailed qualitative and quantitative assessment of circuit designs, design comparison, and design optimisation. The ability to identify leakage transitions is an important step in the process of optimising DNA circuit layouts where the aim is to minimise the computational error inherent in a circuit while minimising the area of the circuit. Our 2D modelling approach of DNA walker circuits relies on coloured stochastic Petri nets which enable functionality, topology and dimensionality all to be integrated in one two-dimensional model. Our modelling and analysis approach can be easily extended to 3-dimensional walker systems.

Using Petri Net Tools to Study Properties and Dynamics of Biological Systems

PubMed Central

Peleg, Mor; Rubin, Daniel; Altman, Russ B.

2005-01-01

Petri Nets (PNs) and their extensions are promising methods for modeling and simulating biological systems. We surveyed PN formalisms and tools and compared them based on their mathematical capabilities as well as by their appropriateness to represent typical biological processes. We measured the ability of these tools to model specific features of biological systems and answer a set of biological questions that we defined. We found that different tools are required to provide all capabilities that we assessed. We created software to translate a generic PN model into most of the formalisms and tools discussed. We have also made available three models and suggest that a library of such models would catalyze progress in qualitative modeling via PNs. Development and wide adoption of common formats would enable researchers to share models and use different tools to analyze them without the need to convert to proprietary formats. PMID:15561791

Cell Illustrator 4.0: a computational platform for systems biology.

PubMed

Nagasaki, Masao; Saito, Ayumu; Jeong, Euna; Li, Chen; Kojima, Kaname; Ikeda, Emi; Miyano, Satoru

2010-01-01

Cell Illustrator is a software platform for Systems Biology that uses the concept of Petri net for modeling and simulating biopathways. It is intended for biological scientists working at bench. The latest version of Cell Illustrator 4.0 uses Java Web Start technology and is enhanced with new capabilities, including: automatic graph grid layout algorithms using ontology information; tools using Cell System Markup Language (CSML) 3.0 and Cell System Ontology 3.0; parameter search module; high-performance simulation module; CSML database management system; conversion from CSML model to programming languages (FORTRAN, C, C++, Java, Python and Perl); import from SBML, CellML, and BioPAX; and, export to SVG and HTML. Cell Illustrator employs an extension of hybrid Petri net in an object-oriented style so that biopathway models can include objects such as DNA sequence, molecular density, 3D localization information, transcription with frame-shift, translation with codon table, as well as biochemical reactions.

Polynomial algebra of discrete models in systems biology.

PubMed

Veliz-Cuba, Alan; Jarrah, Abdul Salam; Laubenbacher, Reinhard

2010-07-01

An increasing number of discrete mathematical models are being published in Systems Biology, ranging from Boolean network models to logical models and Petri nets. They are used to model a variety of biochemical networks, such as metabolic networks, gene regulatory networks and signal transduction networks. There is increasing evidence that such models can capture key dynamic features of biological networks and can be used successfully for hypothesis generation. This article provides a unified framework that can aid the mathematical analysis of Boolean network models, logical models and Petri nets. They can be represented as polynomial dynamical systems, which allows the use of a variety of mathematical tools from computer algebra for their analysis. Algorithms are presented for the translation into polynomial dynamical systems. Examples are given of how polynomial algebra can be used for the model analysis. alanavc@vt.edu Supplementary data are available at Bioinformatics online.

Nested Interrupt Analysis of Low Cost and High Performance Embedded Systems Using GSPN Framework

NASA Astrophysics Data System (ADS)

Lin, Cheng-Min

Interrupt service routines are a key technology for embedded systems. In this paper, we introduce the standard approach for using Generalized Stochastic Petri Nets (GSPNs) as a high-level model for generating CTMC Continuous-Time Markov Chains (CTMCs) and then use Markov Reward Models (MRMs) to compute the performance for embedded systems. This framework is employed to analyze two embedded controllers with low cost and high performance, ARM7 and Cortex-M3. Cortex-M3 is designed with a tail-chaining mechanism to improve the performance of ARM7 when a nested interrupt occurs on an embedded controller. The Platform Independent Petri net Editor 2 (PIPE2) tool is used to model and evaluate the controllers in terms of power consumption and interrupt overhead performance. Using numerical results, in spite of the power consumption or interrupt overhead, Cortex-M3 performs better than ARM7.

A fuzzy Petri-net-based mode identification algorithm for fault diagnosis of complex systems

NASA Astrophysics Data System (ADS)

Propes, Nicholas C.; Vachtsevanos, George

2003-08-01

Complex dynamical systems such as aircraft, manufacturing systems, chillers, motor vehicles, submarines, etc. exhibit continuous and event-driven dynamics. These systems undergo several discrete operating modes from startup to shutdown. For example, a certain shipboard system may be operating at half load or full load or may be at start-up or shutdown. Of particular interest are extreme or "shock" operating conditions, which tend to severely impact fault diagnosis or the progression of a fault leading to a failure. Fault conditions are strongly dependent on the operating mode. Therefore, it is essential that in any diagnostic/prognostic architecture, the operating mode be identified as accurately as possible so that such functions as feature extraction, diagnostics, prognostics, etc. can be correlated with the predominant operating conditions. This paper introduces a mode identification methodology that incorporates both time- and event-driven information about the process. A fuzzy Petri net is used to represent the possible successive mode transitions and to detect events from processed sensor signals signifying a mode change. The operating mode is initialized and verified by analysis of the time-driven dynamics through a fuzzy logic classifier. An evidence combiner module is used to combine the results from both the fuzzy Petri net and the fuzzy logic classifier to determine the mode. Unlike most event-driven mode identifiers, this architecture will provide automatic mode initialization through the fuzzy logic classifier and robustness through the combining of evidence of the two algorithms. The mode identification methodology is applied to an AC Plant typically found as a component of a shipboard system.

Event-driven management algorithm of an Engineering documents circulation system

NASA Astrophysics Data System (ADS)

Kuzenkov, V.; Zebzeev, A.; Gromakov, E.

2015-04-01

Development methodology of an engineering documents circulation system in the design company is reviewed. Discrete event-driven automatic models using description algorithms of project management is offered. Petri net use for dynamic design of projects is offered.

Modelling a radiology department service using a VDL integrated approach.

PubMed

Guglielmino, Maria Gabriella; Celano, Giovanni; Costa, Antonio; Fichera, Sergio

2009-01-01

The healthcare industry is facing several challenges such as the reduction of costs and quality improvement of the provided services. Engineering studies could be very useful in supporting organizational and management processes. Healthcare service efficiency depends on a strong collaboration between clinical and engineering experts, especially when it comes to analyzing the system and its constraints in detail and subsequently, when it comes to deciding on the reengineering of some key activities. The purpose of this paper is to propose a case study showing how a mix of representation tools allow a manager of a radiology department to solve some human and technological resource re-organizational issues, which have to be faced due to the introduction of a new technology and a new portfolio of services. In order to simulate the activities within the radiology department and examine the relationship between human and technological resources, different visual diagrammatic language (VDL) techniques have been implemented to get knowledge about the heterogeneous factors related to the healthcare service delivery. In particular, flow charts, IDEFO diagrams and Petri nets have been integrated each other with success as a modelisation tools. The simulation study performed through the application of the aforementioned VDL techniques suggests the opportunity of re-organizing the nurse activities within the radiology department. The re-organization of a healthcare service and in particular of a radiology department by means of joint flow charts, IDEF0 diagrams and Petri nets is a poorly investigated topic in literature. This paper demonstrates how flow charts and IDEF0 can help people working within the department to understand the weak points of their organization and constitute an efficient base of knowledge for the implementation of a Petri net aimed at improving the departmental performance.

Modeling Cyber Conflicts Using an Extended Petri Net Formalism

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zakrzewska, Anita N; Ferragut, Erik M

2011-01-01

When threatened by automated attacks, critical systems that require human-controlled responses have difficulty making optimal responses and adapting protections in real- time and may therefore be overwhelmed. Consequently, experts have called for the development of automatic real-time reaction capabilities. However, a technical gap exists in the modeling and analysis of cyber conflicts to automatically understand the repercussions of responses. There is a need for modeling cyber assets that accounts for concurrent behavior, incomplete information, and payoff functions. Furthermore, we address this need by extending the Petri net formalism to allow real-time cyber conflicts to be modeled in a way thatmore » is expressive and concise. This formalism includes transitions controlled by players as well as firing rates attached to transitions. This allows us to model both player actions and factors that are beyond the control of players in real-time. We show that our formalism is able to represent situational aware- ness, concurrent actions, incomplete information and objective functions. These factors make it well-suited to modeling cyber conflicts in a way that allows for useful analysis. MITRE has compiled the Common Attack Pattern Enumera- tion and Classification (CAPEC), an extensive list of cyber attacks at various levels of abstraction. CAPEC includes factors such as attack prerequisites, possible countermeasures, and attack goals. These elements are vital to understanding cyber attacks and to generating the corresponding real-time responses. We demonstrate that the formalism can be used to extract precise models of cyber attacks from CAPEC. Several case studies show that our Petri net formalism is more expressive than other models, such as attack graphs, for modeling cyber conflicts and that it is amenable to exploring cyber strategies.« less

Ensuring Patient Safety by using Colored Petri Net Simulation in the Design of Heterogeneous, Multi-Vendor, Integrated, Life-Critical Wireless (802.x) Patient Care Device Networks.

PubMed

Sloane, Elliot; Gehlot, Vijay

2005-01-01

Hospitals and manufacturers are designing and deploying the IEEE 802.x wireless technologies in medical devices to promote patient mobility and flexible facility use. There is little information, however, on the reliability or ultimate safety of connecting multiple wireless life-critical medical devices from multiple vendors using commercial 802.11a, 802.11b, 802.11g or pre-802.11n devices. It is believed that 802.11-type devices can introduce unintended life-threatening risks unless delivery of critical patient alarms to central monitoring systems and/or clinical personnel is assured by proper use of 802.11e Quality of Service (QoS) methods. Petri net tools can be used to simulate all possible states and transitions between devices and/or systems in a wireless device network, and can identify failure modes in advance. Colored Petri Net (CPN) tools are ideal, in fact, as they allow tracking and controlling each message in a network based on pre-selected criteria. This paper describes a research project using CPN to simulate and validate alarm integrity in a small multi-modality wireless patient monitoring system. A 20-monitor wireless patient monitoring network is created in two versions: one with non-prioritized 802.x CSM protocols and the second with simulated Quality of Service (QoS) capabilities similar to 802.11e (i.e., the second network allows message priority management.) In the standard 802.x network, dangerous heart arrhythmia and pulse oximetry alarms could not be reliably and rapidly communicated, but the second network's QoS priority management reduced that risk significantly.

Constant speed control of four-stroke micro internal combustion swing engine

NASA Astrophysics Data System (ADS)

Gao, Dedong; Lei, Yong; Zhu, Honghai; Ni, Jun

2015-09-01

The increasing demands on safety, emission and fuel consumption require more accurate control models of micro internal combustion swing engine (MICSE). The objective of this paper is to investigate the constant speed control models of four-stroke MICSE. The operation principle of the four-stroke MICSE is presented based on the description of MICSE prototype. A two-level Petri net based hybrid model is proposed to model the four-stroke MICSE engine cycle. The Petri net subsystem at the upper level controls and synchronizes the four Petri net subsystems at the lower level. The continuous sub-models, including breathing dynamics of intake manifold, thermodynamics of the chamber and dynamics of the torque generation, are investigated and integrated with the discrete model in MATLAB Simulink. Through the comparison of experimental data and simulated DC voltage output, it is demonstrated that the hybrid model is valid for the four-stroke MICSE system. A nonlinear model is obtained from the cycle average data via the regression method, and it is linearized around a given nominal equilibrium point for the controller design. The feedback controller of the spark timing and valve duration timing is designed with a sequential loop closing design approach. The simulation of the sequential loop closure control design applied to the hybrid model is implemented in MATLAB. The simulation results show that the system is able to reach its desired operating point within 0.2 s, and the designed controller shows good MICSE engine performance with a constant speed. This paper presents the constant speed control models of four-stroke MICSE and carries out the simulation tests, the models and the simulation results can be used for further study on the precision control of four-stroke MICSE.

Robustness analysis of non-ordinary Petri nets for flexible assembly/disassembly processes based on structural decomposition

NASA Astrophysics Data System (ADS)

Hsieh, Fu-Shiung

2011-03-01

Design of robust supervisory controllers for manufacturing systems with unreliable resources has received significant attention recently. Robustness analysis provides an alternative way to analyse a perturbed system to quickly respond to resource failures. Although we have analysed the robustness properties of several subclasses of ordinary Petri nets (PNs), analysis for non-ordinary PNs has not been done. Non-ordinary PNs have weighted arcs and have the advantage to compactly model operations requiring multiple parts or resources. In this article, we consider a class of flexible assembly/disassembly manufacturing systems and propose a non-ordinary flexible assembly/disassembly Petri net (NFADPN) model for this class of systems. As the class of flexible assembly/disassembly manufacturing systems can be regarded as the integration and interactions of a set of assembly/disassembly subprocesses, a bottom-up approach is adopted in this article to construct the NFADPN models. Due to the routing flexibility in NFADPN, there may exist different ways to accomplish the tasks. To characterise different ways to accomplish the tasks, we propose the concept of completely connected subprocesses. As long as there exists a set of completely connected subprocesses for certain type of products, the production of that type of products can still be maintained without requiring the whole NFADPN to be live. To take advantage of the alternative routes without enforcing liveness for the whole system, we generalise the concept of persistent production proposed to NFADPN. We propose a condition for persistent production based on the concept of completely connected subprocesses. We extend robustness analysis to NFADPN by exploiting its structure. We identify several patterns of resource failures and characterise the conditions to maintain operation in the presence of resource failures.

Modelling and Analysis of the Feeding Regimen Induced Entrainment of Hepatocyte Circadian Oscillators Using Petri Nets

PubMed Central

Tareen, Samar Hayat Khan; Ahmad, Jamil

2015-01-01

Circadian rhythms are certain periodic behaviours exhibited by living organism at different levels, including cellular and system-wide scales. Recent studies have found that the circadian rhythms of several peripheral organs in mammals, such as the liver, are able to entrain their clocks to received signals independent of other system level clocks, in particular when responding to signals generated during feeding. These studies have found SIRT1, PARP1, and HSF1 proteins to be the major influencers of the core CLOCKBMAL1:PER-CRY circadian clock. These entities, along with abstracted feeding induced signals were modelled collectively in this study using Petri Nets. The properties of the model show that the circadian system itself is strongly robust, and is able to continually evolve. The modelled feeding regimens suggest that the usual 3 meals/day and 2 meals/day feeding regimens are beneficial with any more or less meals/day negatively affecting the system. PMID:25789928

Modelling safety of gantry crane operations using Petri nets.

PubMed

Singh, Karmveer; Raj, Navneet; Sahu, S K; Behera, R K; Sarkar, Sobhan; Maiti, J

2017-03-01

Being a powerful tool in modelling industrial and service operations, Petri net (PN) has been extremely used in different domains, but its application in safety study is limited. In this study, we model the gantry crane operations used for industrial activities using generalized stochastic PNs. The complete cycle of operations of the gantry crane is split into three parts namely inspection and loading, movement of load, and unloading of load. PN models are developed for all three parts and the whole system as well. The developed PN models have captured the safety issues through reachability tree. The hazardous states are identified and how they ultimately lead to some unwanted accidents is demonstrated. The possibility of falling of load and failure of hook, sling, attachment and hoist rope are identified. Possible suggestions based on the study are presented for redesign of the system. For example, mechanical stoppage of operations in case of loosely connected load, and warning system for use of wrong buttons is tested using modified models.

Distributed state-space generation of discrete-state stochastic models

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco; Gluckman, Joshua; Nicol, David

1995-01-01

High-level formalisms such as stochastic Petri nets can be used to model complex systems. Analysis of logical and numerical properties of these models of ten requires the generation and storage of the entire underlying state space. This imposes practical limitations on the types of systems which can be modeled. Because of the vast amount of memory consumed, we investigate distributed algorithms for the generation of state space graphs. The distributed construction allows us to take advantage of the combined memory readily available on a network of workstations. The key technical problem is to find effective methods for on-the-fly partitioning, so that the state space is evenly distributed among processors. In this paper we report on the implementation of a distributed state-space generator that may be linked to a number of existing system modeling tools. We discuss partitioning strategies in the context of Petri net models, and report on performance observed on a network of workstations, as well as on a distributed memory multi-computer.

Petri net-based method for the analysis of the dynamics of signal propagation in signaling pathways.

PubMed

Hardy, Simon; Robillard, Pierre N

2008-01-15

Cellular signaling networks are dynamic systems that propagate and process information, and, ultimately, cause phenotypical responses. Understanding the circuitry of the information flow in cells is one of the keys to understanding complex cellular processes. The development of computational quantitative models is a promising avenue for attaining this goal. Not only does the analysis of the simulation data based on the concentration variations of biological compounds yields information about systemic state changes, but it is also very helpful for obtaining information about the dynamics of signal propagation. This article introduces a new method for analyzing the dynamics of signal propagation in signaling pathways using Petri net theory. The method is demonstrated with the Ca(2+)/calmodulin-dependent protein kinase II (CaMKII) regulation network. The results constitute temporal information about signal propagation in the network, a simplified graphical representation of the network and of the signal propagation dynamics and a characterization of some signaling routes as regulation motifs.

QoS measurement of workflow-based web service compositions using Colored Petri net.

PubMed

Nematzadeh, Hossein; Motameni, Homayun; Mohamad, Radziah; Nematzadeh, Zahra

2014-01-01

Workflow-based web service compositions (WB-WSCs) is one of the main composition categories in service oriented architecture (SOA). Eflow, polymorphic process model (PPM), and business process execution language (BPEL) are the main techniques of the category of WB-WSCs. Due to maturity of web services, measuring the quality of composite web services being developed by different techniques becomes one of the most important challenges in today's web environments. Business should try to provide good quality regarding the customers' requirements to a composed web service. Thus, quality of service (QoS) which refers to nonfunctional parameters is important to be measured since the quality degree of a certain web service composition could be achieved. This paper tried to find a deterministic analytical method for dependability and performance measurement using Colored Petri net (CPN) with explicit routing constructs and application of theory of probability. A computer tool called WSET was also developed for modeling and supporting QoS measurement through simulation.

Simulation-Based Validation of the p53 Transcriptional Activity with Hybrid Functional Petri Net.

PubMed

Doi, Atsushi; Nagasaki, Masao; Matsuno, Hiroshi; Miyano, Satoru

2011-01-01

MDM2 and p19ARF are essential proteins in cancer pathways forming a complex with protein p53 to control the transcriptional activity of protein p53. It is confirmed that protein p53 loses its transcriptional activity by forming the functional dimer with protein MDM2. However, it is still unclear that protein p53 keeps its transcriptional activity when it forms the trimer with proteins MDM2 and p19ARF. We have observed mutual behaviors among genes p53, MDM2, p19ARF and their products on a computational model with hybrid functional Petri net (HFPN) which is constructed based on information described in the literature. The simulation results suggested that protein p53 should have the transcriptional activity in the forms of the trimer of proteins p53, MDM2, and p19ARF. This paper also discusses the advantages of HFPN based modeling method in terms of pathway description for simulations.

Applications of colored petri net and genetic algorithms to cluster tool scheduling

NASA Astrophysics Data System (ADS)

Liu, Tung-Kuan; Kuo, Chih-Jen; Hsiao, Yung-Chin; Tsai, Jinn-Tsong; Chou, Jyh-Horng

2005-12-01

In this paper, we propose a method, which uses Coloured Petri Net (CPN) and genetic algorithm (GA) to obtain an optimal deadlock-free schedule and to solve re-entrant problem for the flexible process of the cluster tool. The process of the cluster tool for producing a wafer usually can be classified into three types: 1) sequential process, 2) parallel process, and 3) sequential parallel process. But these processes are not economical enough to produce a variety of wafers in small volume. Therefore, this paper will propose the flexible process where the operations of fabricating wafers are randomly arranged to achieve the best utilization of the cluster tool. However, the flexible process may have deadlock and re-entrant problems which can be detected by CPN. On the other hand, GAs have been applied to find the optimal schedule for many types of manufacturing processes. Therefore, we successfully integrate CPN and GAs to obtain an optimal schedule with the deadlock and re-entrant problems for the flexible process of the cluster tool.

Reliability apportionment approach for spacecraft solar array using fuzzy reasoning Petri net and fuzzy comprehensive evaluation

NASA Astrophysics Data System (ADS)

Wu, Jianing; Yan, Shaoze; Xie, Liyang; Gao, Peng

2012-07-01

The reliability apportionment of spacecraft solar array is of significant importance for spacecraft designers in the early stage of design. However, it is difficult to use the existing methods to resolve reliability apportionment problem because of the data insufficiency and the uncertainty of the relations among the components in the mechanical system. This paper proposes a new method which combines the fuzzy comprehensive evaluation with fuzzy reasoning Petri net (FRPN) to accomplish the reliability apportionment of the solar array. The proposed method extends the previous fuzzy methods and focuses on the characteristics of the subsystems and the intrinsic associations among the components. The analysis results show that the synchronization mechanism may obtain the highest reliability value and the solar panels and hinges may get the lowest reliability before design and manufacturing. Our developed method is of practical significance for the reliability apportionment of solar array where the design information has not been clearly identified, particularly in early stage of design.

Fault detection and initial state verification by linear programming for a class of Petri nets

NASA Technical Reports Server (NTRS)

Rachell, Traxon; Meyer, David G.

1992-01-01

The authors present an algorithmic approach to determining when the marking of a LSMG (live safe marked graph) or a LSFC (live safe free choice) net is in the set of live safe markings M. Hence, once the marking of a net is determined to be in M, then if at some time thereafter the marking of this net is determined not to be in M, this indicates a fault. It is shown how linear programming can be used to determine if m is an element of M. The worst-case computational complexity of each algorithm is bounded by the number of linear programs necessary to compute.

Electronic Business Transaction Infrastructure Analysis Using Petri Nets and Simulation

ERIC Educational Resources Information Center

Feller, Andrew Lee

2010-01-01

Rapid growth in eBusiness has made industry and commerce increasingly dependent on the hardware and software infrastructure that enables high-volume transaction processing across the Internet. Large transaction volumes at major industrial-firm data centers rely on robust transaction protocols and adequately provisioned hardware capacity to ensure…

Adaptive Decision Making and Coordination in Variable Structure Organizations

DTIC Science & Technology

1994-09-01

behavior of the net. The design problem is addressed by (a) focusing on algorithms that relate structural properties of’ the Petri Net model to... behavioral characteristics; and (b) by incorporating design requirements in the Lattice algorithm. ’K94-30756 9 4 9 2 P 0 8 II083II Bl l~ll i1111 I! 14...the more resource- consuming the process is. The architecture designer has to deal with these two parameters and perform some tradeoffs. The more

Principles of E-network modelling of heterogeneous systems

NASA Astrophysics Data System (ADS)

Tarakanov, D.; Tsapko, I.; Tsapko, S.; Buldygin, R.

2016-04-01

The present article is concerned with the analytical and simulation modelling of heterogeneous technical systems using E-network mathematical apparatus (the expansion of Petri nets). The distinguishing feature of the given system is the presence of the module6 which identifies the parameters of the controlled object as well as the external environment.

Performance modeling of automated manufacturing systems

NASA Astrophysics Data System (ADS)

Viswanadham, N.; Narahari, Y.

A unified and systematic treatment is presented of modeling methodologies and analysis techniques for performance evaluation of automated manufacturing systems. The book is the first treatment of the mathematical modeling of manufacturing systems. Automated manufacturing systems are surveyed and three principal analytical modeling paradigms are discussed: Markov chains, queues and queueing networks, and Petri nets.

Reliability analysis method of a solar array by using fault tree analysis and fuzzy reasoning Petri net

NASA Astrophysics Data System (ADS)

Wu, Jianing; Yan, Shaoze; Xie, Liyang

2011-12-01

To address the impact of solar array anomalies, it is important to perform analysis of the solar array reliability. This paper establishes the fault tree analysis (FTA) and fuzzy reasoning Petri net (FRPN) models of a solar array mechanical system and analyzes reliability to find mechanisms of the solar array fault. The index final truth degree (FTD) and cosine matching function (CMF) are employed to resolve the issue of how to evaluate the importance and influence of different faults. So an improvement reliability analysis method is developed by means of the sorting of FTD and CMF. An example is analyzed using the proposed method. The analysis results show that harsh thermal environment and impact caused by particles in space are the most vital causes of the solar array fault. Furthermore, other fault modes and the corresponding improvement methods are discussed. The results reported in this paper could be useful for the spacecraft designers, particularly, in the process of redesigning the solar array and scheduling its reliability growth plan.

Architectures for intelligent machines

NASA Technical Reports Server (NTRS)

Saridis, George N.

1991-01-01

The theory of intelligent machines has been recently reformulated to incorporate new architectures that are using neural and Petri nets. The analytic functions of an intelligent machine are implemented by intelligent controls, using entropy as a measure. The resulting hierarchical control structure is based on the principle of increasing precision with decreasing intelligence. Each of the three levels of the intelligent control is using different architectures, in order to satisfy the requirements of the principle: the organization level is moduled after a Boltzmann machine for abstract reasoning, task planning and decision making; the coordination level is composed of a number of Petri net transducers supervised, for command exchange, by a dispatcher, which also serves as an interface to the organization level; the execution level, include the sensory, planning for navigation and control hardware which interacts one-to-one with the appropriate coordinators, while a VME bus provides a channel for database exchange among the several devices. This system is currently implemented on a robotic transporter, designed for space construction at the CIRSSE laboratories at the Rensselaer Polytechnic Institute. The progress of its development is reported.

Design and Analysis of a Petri Net Model of the Von Hippel-Lindau (VHL) Tumor Suppressor Interaction Network

PubMed Central

Minervini, Giovanni; Panizzoni, Elisabetta; Giollo, Manuel; Masiero, Alessandro; Ferrari, Carlo; Tosatto, Silvio C. E.

2014-01-01

Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related to germline inactivation of the homonymous tumor suppressor pVHL. The best characterized function of pVHL is the ubiquitination dependent degradation of Hypoxia Inducible Factor (HIF) via the proteasome. It is also involved in several cellular pathways acting as a molecular hub and interacting with more than 200 different proteins. Molecular details of pVHL plasticity remain in large part unknown. Here, we present a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways. PMID:24886840

Design and analysis of a Petri net model of the Von Hippel-Lindau (VHL) tumor suppressor interaction network.

PubMed

Minervini, Giovanni; Panizzoni, Elisabetta; Giollo, Manuel; Masiero, Alessandro; Ferrari, Carlo; Tosatto, Silvio C E

2014-01-01

Von Hippel-Lindau (VHL) syndrome is a hereditary condition predisposing to the development of different cancer forms, related to germline inactivation of the homonymous tumor suppressor pVHL. The best characterized function of pVHL is the ubiquitination dependent degradation of Hypoxia Inducible Factor (HIF) via the proteasome. It is also involved in several cellular pathways acting as a molecular hub and interacting with more than 200 different proteins. Molecular details of pVHL plasticity remain in large part unknown. Here, we present a novel manually curated Petri Net (PN) model of the main pVHL functional pathways. The model was built using functional information derived from the literature. It includes all major pVHL functions and is able to credibly reproduce VHL syndrome at the molecular level. The reliability of the PN model also allowed in silico knockout experiments, driven by previous model analysis. Interestingly, PN analysis suggests that the variability of different VHL manifestations is correlated with the concomitant inactivation of different metabolic pathways.

The role of Fenton reaction in ROS-induced toxicity underlying atherosclerosis - modeled and analyzed using a Petri net-based approach.

PubMed

Formanowicz, Dorota; Radom, Marcin; Rybarczyk, Agnieszka; Formanowicz, Piotr

2018-03-01

The superoxide-driven Fenton reaction plays an important role in the transformation of poorly reactive radicals into highly reactive ones. These highly reactive species (ROS), especially hydroxyl radicals can lead to many disturbances contributing to the endothelial dysfunction being a starting point for atherosclerosis. Although, iron has been identified as a possible culprit influencing formation of ROS, its significance in this process is still debatable. To better understand this phenomenon, the influence of blockade of Fenton reaction in a proposed Petri net-based model of the selected aspects of the iron ROS-induced toxicity in atherosclerosis has been evaluated. As a result of the blockade of iron ions formation in the model, even up to 70% of the paths leading to the progression of atherosclerosis in this model has been blocked. In addition, after adding to the model, the blockade of the lipids peroxidation paths, progression of atherosclerotic plaque has been not observed. This allowed to conclude that the superoxide-driven Fenton reaction plays a significant role in the atherosclerosis. Copyright © 2018 Elsevier B.V. All rights reserved.

Designing software for operational decision support through coloured Petri nets

NASA Astrophysics Data System (ADS)

Maggi, F. M.; Westergaard, M.

2017-05-01

Operational support provides, during the execution of a business process, replies to questions such as 'how do I end the execution of the process in the cheapest way?' and 'is my execution compliant with some expected behaviour?' These questions may be asked several times during a single execution and, to answer them, dedicated software components (the so-called operational support providers) need to be invoked. Therefore, an infrastructure is needed to handle multiple providers, maintain data between queries about the same execution and discard information when it is no longer needed. In this paper, we use coloured Petri nets (CPNs) to model and analyse software implementing such an infrastructure. This analysis is needed to clarify the requirements before implementation and to guarantee that the resulting software is correct. To this aim, we present techniques to represent and analyse state spaces with 250 million states on a normal PC. We show how the specified requirements have been implemented as a plug-in of the process mining tool ProM and how the operational support in ProM can be used in combination with an existing operational support provider.

Method for hierarchical modeling of the command of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Ausfelder, Christian; Castelain, Emmanuel; Gentina, Jean-Claude

1994-04-01

The present paper focuses on the modeling of the command and proposes a hierarchical and modular approach which is oriented on the physical structure of FMS. The requirements issuing from monitoring of FMS are discussed and integrated in the proposed model. Its modularity makes the approach open for extensions concerning as well the production resources as the products. As a modeling tool, we have chosen Object Petri nets. The first part of the paper describes desirable features of an FMS command such as safety, robustness, and adaptability. As it is shown, these features result from the flexibility of the installation. The modeling method presented in the second part of the paper begins with a structural analysis of FMS and defines a natural command hierarchy, where the coordination of the production process, the synchronization of production resources on products, and the internal coordination are treated separately. The method is rigorous and leads to a structured and modular Petri net model which can be used for FMS simulation or translated into the final command code.

A methodological approach for using high-level Petri Nets to model the immune system response.

PubMed

Pennisi, Marzio; Cavalieri, Salvatore; Motta, Santo; Pappalardo, Francesco

2016-12-22

Mathematical and computational models showed to be a very important support tool for the comprehension of the immune system response against pathogens. Models and simulations allowed to study the immune system behavior, to test biological hypotheses about diseases and infection dynamics, and to improve and optimize novel and existing drugs and vaccines. Continuous models, mainly based on differential equations, usually allow to qualitatively study the system but lack in description; conversely discrete models, such as agent based models and cellular automata, permit to describe in detail entities properties at the cost of losing most qualitative analyses. Petri Nets (PN) are a graphical modeling tool developed to model concurrency and synchronization in distributed systems. Their use has become increasingly marked also thanks to the introduction in the years of many features and extensions which lead to the born of "high level" PN. We propose a novel methodological approach that is based on high level PN, and in particular on Colored Petri Nets (CPN), that can be used to model the immune system response at the cellular scale. To demonstrate the potentiality of the approach we provide a simple model of the humoral immune system response that is able of reproducing some of the most complex well-known features of the adaptive response like memory and specificity features. The methodology we present has advantages of both the two classical approaches based on continuous and discrete models, since it allows to gain good level of granularity in the description of cells behavior without losing the possibility of having a qualitative analysis. Furthermore, the presented methodology based on CPN allows the adoption of the same graphical modeling technique well known to life scientists that use PN for the modeling of signaling pathways. Finally, such an approach may open the floodgates to the realization of multi scale models that integrate both signaling pathways (intra cellular) models and cellular (population) models built upon the same technique and software.

The fundamental closed-form solution of control-related states of kth order S3PR system with left-side non-sharing resource places of Petri nets

NASA Astrophysics Data System (ADS)

Chao, Daniel Yuh; Yu, Tsung Hsien

2016-01-01

Due to the state explosion problem, it has been unimaginable to enumerate reachable states for Petri nets. Chao broke the barrier earlier by developing the very first closed-form solution of the number of reachable and other states for marked graphs and the kth order system. Instead of using first-met bad marking, we propose 'the moment to launch resource allocation' (MLR) as a partial deadlock avoidance policy for a large, real-time dynamic resource allocation system. Presently, we can use the future deadlock ratio of the current state as the indicator of MLR due to which the ratio can be obtained real-time by a closed-form formula. This paper progresses the application of an MLR concept one step further on Gen-Left kth order systems (one non-sharing resource place in any position of the left-side process), which is also the most fundamental asymmetric net structure, by the construction of the system's closed-form solution of the control-related states (reachable, forbidden, live and deadlock states) with a formula depending on the parameters of k and the location of the non-sharing resource. Here, we kick off a new era of real-time, dynamic resource allocation decisions by constructing a generalisation formula of kth order systems (Gen-Left) with r* on the left side but at arbitrary locations.

On Complex Networks Representation and Computation of Hydrologycal Quantities

NASA Astrophysics Data System (ADS)

Serafin, F.; Bancheri, M.; David, O.; Rigon, R.

2017-12-01

Water is our blue gold. Despite results of discovery-based science keep warning public opinion about the looming worldwide water crisis, water is still treated as a not worth taking resource. Could a different multi-scale perspective affect environmental decision-making more deeply? Can also a further pairing to a new graphical representation of processes interaction sway decision-making more effectively and public opinion consequently?This abstract introduces a complex networks driven way to represent catchments eco-hydrology and related flexible informatics to manage it. The representation is built upon mathematical category. A category is an algebraic structure that comprises "objects" linked by "arrows". It is an evolution of Petri Nets said Time Continuous Petri Nets (TCPN). It aims to display (water) budgets processes and catchment interactions using explicative and self-contained symbolism. The result improves readability of physical processes compared to current descriptions. The IT perspective hinges on the Object Modeling System (OMS) v3. The latter is a non-invasive flexible environmental modeling framework designed to support component-based model development. The implementation of a Directed Acyclic Graph (DAG) data structure, named Net3, has recently enhanced its flexibility. Net3 represents interacting systems as complex networks: vertices match up with any sort of time evolving quantity; edges correspond to their data (fluxes) interchange. It currently hosts JGrass-NewAge components, and those implementing travel time analysis of fluxes. Further bio-physical or management oriented components can be easily added.This talk introduces both graphical representation and related informatics exercising actual applications and examples.

Knowledge acquisition and representation using fuzzy evidential reasoning and dynamic adaptive fuzzy Petri nets.

PubMed

Liu, Hu-Chen; Liu, Long; Lin, Qing-Lian; Liu, Nan

2013-06-01

The two most important issues of expert systems are the acquisition of domain experts' professional knowledge and the representation and reasoning of the knowledge rules that have been identified. First, during expert knowledge acquisition processes, the domain expert panel often demonstrates different experience and knowledge from one another and produces different types of knowledge information such as complete and incomplete, precise and imprecise, and known and unknown because of its cross-functional and multidisciplinary nature. Second, as a promising tool for knowledge representation and reasoning, fuzzy Petri nets (FPNs) still suffer a couple of deficiencies. The parameters in current FPN models could not accurately represent the increasingly complex knowledge-based systems, and the rules in most existing knowledge inference frameworks could not be dynamically adjustable according to propositions' variation as human cognition and thinking. In this paper, we present a knowledge acquisition and representation approach using the fuzzy evidential reasoning approach and dynamic adaptive FPNs to solve the problems mentioned above. As is illustrated by the numerical example, the proposed approach can well capture experts' diversity experience, enhance the knowledge representation power, and reason the rule-based knowledge more intelligently.

Contribution to the modelling and analysis of logistics system performance by Petri nets and simulation models: Application in a supply chain

NASA Astrophysics Data System (ADS)

Azougagh, Yassine; Benhida, Khalid; Elfezazi, Said

2016-02-01

In this paper, the focus is on studying the performance of complex systems in a supply chain context by developing a structured modelling approach based on the methodology ASDI (Analysis, Specification, Design and Implementation) by combining the modelling by Petri nets and simulation using ARENA. The linear approach typically followed in conducting of this kind of problems has to cope with a difficulty of modelling due to the complexity and the number of parameters of concern. Therefore, the approach used in this work is able to structure modelling a way to cover all aspects of the performance study. The modelling structured approach is first introduced before being applied to the case of an industrial system in the field of phosphate. Results of the performance indicators obtained from the models developed, permitted to test the behaviour and fluctuations of this system and to develop improved models of the current situation. In addition, in this paper, it was shown how Arena software can be adopted to simulate complex systems effectively. The method in this research can be applied to investigate various improvements scenarios and their consequences before implementing them in reality.

Reliability prediction of ontology-based service compositions using Petri net and time series models.

PubMed

Li, Jia; Xia, Yunni; Luo, Xin

2014-01-01

OWL-S, one of the most important Semantic Web service ontologies proposed to date, provides a core ontological framework and guidelines for describing the properties and capabilities of their web services in an unambiguous, computer interpretable form. Predicting the reliability of composite service processes specified in OWL-S allows service users to decide whether the process meets the quantitative quality requirement. In this study, we consider the runtime quality of services to be fluctuating and introduce a dynamic framework to predict the runtime reliability of services specified in OWL-S, employing the Non-Markovian stochastic Petri net (NMSPN) and the time series model. The framework includes the following steps: obtaining the historical response times series of individual service components; fitting these series with a autoregressive-moving-average-model (ARMA for short) and predicting the future firing rates of service components; mapping the OWL-S process into a NMSPN model; employing the predicted firing rates as the model input of NMSPN and calculating the normal completion probability as the reliability estimate. In the case study, a comparison between the static model and our approach based on experimental data is presented and it is shown that our approach achieves higher prediction accuracy.

Target-based drug discovery for [Formula: see text]-globin disorders: drug target prediction using quantitative modeling with hybrid functional Petri nets.

PubMed

Mehraei, Mani; Bashirov, Rza; Tüzmen, Şükrü

2016-10-01

Recent molecular studies provide important clues into treatment of [Formula: see text]-thalassemia, sickle-cell anaemia and other [Formula: see text]-globin disorders revealing that increased production of fetal hemoglobin, that is normally suppressed in adulthood, can ameliorate the severity of these diseases. In this paper, we present a novel approach for drug prediction for [Formula: see text]-globin disorders. Our approach is centered upon quantitative modeling of interactions in human fetal-to-adult hemoglobin switch network using hybrid functional Petri nets. In accordance with the reverse pharmacology approach, we pose a hypothesis regarding modulation of specific protein targets that induce [Formula: see text]-globin and consequently fetal hemoglobin. Comparison of simulation results for the proposed strategy with the ones obtained for already existing drugs shows that our strategy is the optimal as it leads to highest level of [Formula: see text]-globin induction and thereby has potential beneficial therapeutic effects on [Formula: see text]-globin disorders. Simulation results enable verification of model coherence demonstrating that it is consistent with qPCR data available for known strategies and/or drugs.

A Petri net model of granulomatous inflammation: implications for IL-10 mediated control of Leishmania donovani infection.

PubMed

Albergante, Luca; Timmis, Jon; Beattie, Lynette; Kaye, Paul M

2013-01-01

Experimental visceral leishmaniasis, caused by infection of mice with the protozoan parasite Leishmania donovani, is characterized by focal accumulation of inflammatory cells in the liver, forming discrete "granulomas" within which the parasite is eventually eliminated. To shed new light on fundamental aspects of granuloma formation and function, we have developed an in silico Petri net model that simulates hepatic granuloma development throughout the course of infection. The model was extensively validated by comparison with data derived from experimental studies in mice, and the model robustness was assessed by a sensitivity analysis. The model recapitulated the progression of disease as seen during experimental infection and also faithfully predicted many of the changes in cellular composition seen within granulomas over time. By conducting in silico experiments, we have identified a previously unappreciated level of inter-granuloma diversity in terms of the development of anti-leishmanial activity. Furthermore, by simulating the impact of IL-10 gene deficiency in a variety of lymphocyte and myeloid cell populations, our data suggest a dominant local regulatory role for IL-10 produced by infected Kupffer cells at the core of the granuloma.

Applying Petri nets to modeling the chemical stage of radiobiological mechanism

NASA Astrophysics Data System (ADS)

Barilla, J.; Lokajíček, M.; Pisaková, H.; Simr, P.

2015-03-01

The chemical stage represents important part of radiological mechanism as double strand breaks of DNA molecules represent main damages leading to final biological effect. These breaks are formed mainly by water radicals arising in clusters formed by densely ionizing ends of primary or secondary charged particles in neighborhood of a DNA molecule. The given effect may be significantly influenced by other species present in water, which may depend on the size and diffusion of corresponding clusters. We have already proposed a model describing the corresponding process (i.e., the combined effect of cluster diffusion and chemical reactions) running in individual radical clusters and influencing the formation probability of main damages (i.e., DSBs). Now a full number of corresponding species will be considered. With the help of Continuous Petri nets it will then be possible to follow the time evolution of corresponding species in individual clusters, which might be important especially in the case of studying the biological effect of very low-LET radiation. The results in deoxygenated water will be presented; the ratio of final and initial contents of corresponding species being in good agreement with values established experimentally.

Coordination control of flexible manufacturing systems

NASA Astrophysics Data System (ADS)

Menon, Satheesh R.

One of the first attempts was made to develop a model driven system for coordination control of Flexible Manufacturing Systems (FMS). The structure and activities of the FMS are modeled using a colored Petri Net based system. This approach has the advantage of being able to model the concurrency inherent in the system. It provides a method for encoding the system state, state transitions and the feasible transitions at any given state. Further structural analysis (for detecting conflicting actions, deadlocks which might occur during operation, etc.) can be performed. The problem is also addressed of implementing and testing the behavior of existing dynamic scheduling approaches in simulations of realistic situations. A simulation architecture was proposed and performance evaluation was carried out for establishing the correctness of the model, stability of the system from a structural (deadlocks) and temporal (boundedness of backlogs) points of view, and for collection of statistics for performance measures such as machine and robot utilizations, average wait times and idle times of resources. A real-time implementation architecture for the coordination controller was also developed and implemented in a software simulated environment. Given the current technology of FMS control, the model-driven colored Petri net-based approach promises to develop a very flexible control environment.

A Petri Net Model of Granulomatous Inflammation: Implications for IL-10 Mediated Control of Leishmania donovani Infection

PubMed Central

Albergante, Luca; Timmis, Jon; Beattie, Lynette; Kaye, Paul M.

2013-01-01

Experimental visceral leishmaniasis, caused by infection of mice with the protozoan parasite Leishmania donovani, is characterized by focal accumulation of inflammatory cells in the liver, forming discrete “granulomas” within which the parasite is eventually eliminated. To shed new light on fundamental aspects of granuloma formation and function, we have developed an in silico Petri net model that simulates hepatic granuloma development throughout the course of infection. The model was extensively validated by comparison with data derived from experimental studies in mice, and the model robustness was assessed by a sensitivity analysis. The model recapitulated the progression of disease as seen during experimental infection and also faithfully predicted many of the changes in cellular composition seen within granulomas over time. By conducting in silico experiments, we have identified a previously unappreciated level of inter-granuloma diversity in terms of the development of anti-leishmanial activity. Furthermore, by simulating the impact of IL-10 gene deficiency in a variety of lymphocyte and myeloid cell populations, our data suggest a dominant local regulatory role for IL-10 produced by infected Kupffer cells at the core of the granuloma. PMID:24363630

A hybrid-system model of the coagulation cascade: simulation, sensitivity, and validation.

PubMed

Makin, Joseph G; Narayanan, Srini

2013-10-01

The process of human blood clotting involves a complex interaction of continuous-time/continuous-state processes and discrete-event/discrete-state phenomena, where the former comprise the various chemical rate equations and the latter comprise both threshold-limited behaviors and binary states (presence/absence of a chemical). Whereas previous blood-clotting models used only continuous dynamics and perforce addressed only portions of the coagulation cascade, we capture both continuous and discrete aspects by modeling it as a hybrid dynamical system. The model was implemented as a hybrid Petri net, a graphical modeling language that extends ordinary Petri nets to cover continuous quantities and continuous-time flows. The primary focus is simulation: (1) fidelity to the clinical data in terms of clotting-factor concentrations and elapsed time; (2) reproduction of known clotting pathologies; and (3) fine-grained predictions which may be used to refine clinical understanding of blood clotting. Next we examine sensitivity to rate-constant perturbation. Finally, we propose a method for titrating between reliance on the model and on prior clinical knowledge. For simplicity, we confine these last two analyses to a critical purely-continuous subsystem of the model.

Process-oriented integration and coordination of healthcare services across organizational boundaries.

PubMed

Tello-Leal, Edgar; Chiotti, Omar; Villarreal, Pablo David

2012-12-01

The paper presents a methodology that follows a top-down approach based on a Model-Driven Architecture for integrating and coordinating healthcare services through cross-organizational processes to enable organizations providing high quality healthcare services and continuous process improvements. The methodology provides a modeling language that enables organizations conceptualizing an integration agreement, and identifying and designing cross-organizational process models. These models are used for the automatic generation of: the private view of processes each organization should perform to fulfill its role in cross-organizational processes, and Colored Petri Net specifications to implement these processes. A multi-agent system platform provides agents able to interpret Colored Petri-Nets to enable the communication between the Healthcare Information Systems for executing the cross-organizational processes. Clinical documents are defined using the HL7 Clinical Document Architecture. This methodology guarantees that important requirements for healthcare services integration and coordination are fulfilled: interoperability between heterogeneous Healthcare Information Systems; ability to cope with changes in cross-organizational processes; guarantee of alignment between the integrated healthcare service solution defined at the organizational level and the solution defined at technological level; and the distributed execution of cross-organizational processes keeping the organizations autonomy.

Yeast pheromone pathway modeling using Petri nets

PubMed Central

2014-01-01

Background Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? Method In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. Conclusion The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not. PMID:25080237

Yeast pheromone pathway modeling using Petri nets.

PubMed

Majumdar, Abhishek; Scott, Stephen D; Deogun, Jitender S; Harris, Steven

2014-01-01

Our environment is composed of biological components of varying magnitude. The relationships between the different biological elements can be represented as a biological network. The process of mating in S. cerevisiae is initiated by secretion of pheromone by one of the cells. Our interest lies in one particular question: how does a cell dynamically adapt the pathway to continue mating under severe environmental changes or under mutation (which might result in the loss of functionality of some proteins known to participate in the pheromone pathway). Our work attempts to answer this question. To achieve this, we first propose a model to simulate the pheromone pathway using Petri nets. Petri nets are directed graphs that can be used for describing and modeling systems characterized as concurrent, asynchronous, distributed, parallel, non-deterministic, and/or stochastic. We then analyze our Petri net-based model of the pathway to investigate the following: 1) Given the model of the pheromone response pathway, under what conditions does the cell respond positively, i.e., mate? 2) What kinds of perturbations in the cell would result in changing a negative response to a positive one? In our model, we classify proteins into two categories: core component proteins (set ψ) and additional proteins (set λ). We randomly generate our model's parameters in repeated simulations. To simulate the pathway, we carry out three different experiments. In the experiments, we simply change the concentration of the additional proteins (λ) available to the cell. The concentration of proteins in ψ is varied consistently from 300 to 400. In Experiment 1, the range of values for λ is set to be 100 to 150. In Experiment 2, it is set to be 151 to 200. In Experiment 3, the set λ is further split into σ and ς, with the idea that proteins in σ are more important than those in ς. The range of values for σ is set to be between 151 to 200 while that of ς is 100 to 150. Decision trees were derived from each of the first two experiments to allow us to more easily analyze the conditions under which the pheromone is expressed. The simulation results reveal that a cell can overcome the detrimental effects of the conditions by using more concentration of additional proteins in λ. The first two experiments provide evidence that employing more concentration of proteins might be one of the ways that the cell uses to adapt itself in inhibiting conditions to facilitate mating. The results of the third experiment reveal that in some case the protein set σ is sufficient in regulating the response of the cell. Results of Experiments 4 and 5 reveal that there are certain conditions (parameters) in the model that are more important in determining whether a cell will respond positively or not.

Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets.

PubMed

Koch, Ina; Nöthen, Joachim; Schleiff, Enrico

2017-01-01

Motivation: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana . We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to nearly all parts of the network, especially to the citric acid cycle. There is a close cooperation of important metabolic pathways, e.g., the de novo synthesis of uridine-5-monophosphate, the γ-aminobutyric acid shunt, and the urea cycle. The presented approach extends the established methods for a feasible interpretation of biological network models, in particular of large and complex models.

Modeling the Metabolism of Arabidopsis thaliana: Application of Network Decomposition and Network Reduction in the Context of Petri Nets

PubMed Central

Koch, Ina; Nöthen, Joachim; Schleiff, Enrico

2017-01-01

Motivation: Arabidopsis thaliana is a well-established model system for the analysis of the basic physiological and metabolic pathways of plants. Nevertheless, the system is not yet fully understood, although many mechanisms are described, and information for many processes exists. However, the combination and interpretation of the large amount of biological data remain a big challenge, not only because data sets for metabolic paths are still incomplete. Moreover, they are often inconsistent, because they are coming from different experiments of various scales, regarding, for example, accuracy and/or significance. Here, theoretical modeling is powerful to formulate hypotheses for pathways and the dynamics of the metabolism, even if the biological data are incomplete. To develop reliable mathematical models they have to be proven for consistency. This is still a challenging task because many verification techniques fail already for middle-sized models. Consequently, new methods, like decomposition methods or reduction approaches, are developed to circumvent this problem. Methods: We present a new semi-quantitative mathematical model of the metabolism of Arabidopsis thaliana. We used the Petri net formalism to express the complex reaction system in a mathematically unique manner. To verify the model for correctness and consistency we applied concepts of network decomposition and network reduction such as transition invariants, common transition pairs, and invariant transition pairs. Results: We formulated the core metabolism of Arabidopsis thaliana based on recent knowledge from literature, including the Calvin cycle, glycolysis and citric acid cycle, glyoxylate cycle, urea cycle, sucrose synthesis, and the starch metabolism. By applying network decomposition and reduction techniques at steady-state conditions, we suggest a straightforward mathematical modeling process. We demonstrate that potential steady-state pathways exist, which provide the fixed carbon to nearly all parts of the network, especially to the citric acid cycle. There is a close cooperation of important metabolic pathways, e.g., the de novo synthesis of uridine-5-monophosphate, the γ-aminobutyric acid shunt, and the urea cycle. The presented approach extends the established methods for a feasible interpretation of biological network models, in particular of large and complex models. PMID:28713420

System Behavior Models: A Survey of Approaches

DTIC Science & Technology

2016-06-01

MODELS: A SURVEY OF APPROACHES by Scott R. Ruppel June 2016 Thesis Advisor: Kristin Giammarco Second Reader: John M. Green THIS PAGE...Thesis 4. TITLE AND SUBTITLE SYSTEM BEHAVIOR MODELS: A SURVEY OF APPROACHES 5. FUNDING NUMBERS 6. AUTHOR(S) Scott R. Ruppel 7. PERFORMING...Monterey Phoenix, Petri nets, behavior modeling, model-based systems engineering, modeling approaches, modeling survey 15. NUMBER OF PAGES 85 16

MONALISA for stochastic simulations of Petri net models of biochemical systems.

PubMed

Balazki, Pavel; Lindauer, Klaus; Einloft, Jens; Ackermann, Jörg; Koch, Ina

2015-07-10

The concept of Petri nets (PN) is widely used in systems biology and allows modeling of complex biochemical systems like metabolic systems, signal transduction pathways, and gene expression networks. In particular, PN allows the topological analysis based on structural properties, which is important and useful when quantitative (kinetic) data are incomplete or unknown. Knowing the kinetic parameters, the simulation of time evolution of such models can help to study the dynamic behavior of the underlying system. If the number of involved entities (molecules) is low, a stochastic simulation should be preferred against the classical deterministic approach of solving ordinary differential equations. The Stochastic Simulation Algorithm (SSA) is a common method for such simulations. The combination of the qualitative and semi-quantitative PN modeling and stochastic analysis techniques provides a valuable approach in the field of systems biology. Here, we describe the implementation of stochastic analysis in a PN environment. We extended MONALISA - an open-source software for creation, visualization and analysis of PN - by several stochastic simulation methods. The simulation module offers four simulation modes, among them the stochastic mode with constant firing rates and Gillespie's algorithm as exact and approximate versions. The simulator is operated by a user-friendly graphical interface and accepts input data such as concentrations and reaction rate constants that are common parameters in the biological context. The key features of the simulation module are visualization of simulation, interactive plotting, export of results into a text file, mathematical expressions for describing simulation parameters, and up to 500 parallel simulations of the same parameter sets. To illustrate the method we discuss a model for insulin receptor recycling as case study. We present a software that combines the modeling power of Petri nets with stochastic simulation of dynamic processes in a user-friendly environment supported by an intuitive graphical interface. The program offers a valuable alternative to modeling, using ordinary differential equations, especially when simulating single-cell experiments with low molecule counts. The ability to use mathematical expressions provides an additional flexibility in describing the simulation parameters. The open-source distribution allows further extensions by third-party developers. The software is cross-platform and is licensed under the Artistic License 2.0.

Nano Petri dishes: a new polystyrene platform for studying cell-nanoengineered surface interactions

NASA Astrophysics Data System (ADS)

Cha, Kyoung Je; Na, Moon-Hee; Kim, Hyung Woo; Kim, Dong Sung

2014-05-01

In this study, we fabricated and fully characterized a new type of polystyrene (PS) cell-culture platform containing nanoengineered surfaces (NES), referred to as a nano Petri dish, which can be used at the transition stage of basic cell-NES interaction studies for clinical applications. Nano-injection molding in this study was used for the mass production of the nano Petri dish having nanopore arrays. The effects of processing parameters of the injection molding on the replication quality of the nanopore arrays were quantitatively evaluated by means of design of experiments based on the Taguchi method. This allowed efficient and reliable cell culture studies by providing large numbers of the same dishes, in addition to removing the fixation step of the NES plates inside the cell-culture container. Physical, chemical and mechanical properties of the NES, as well as cell behavior including attachment and proliferation of human osteosarcoma MG-63 cells on the NES, were then characterized, with and without the oxygen plasma surface treatment.

Dependability and performability analysis

NASA Technical Reports Server (NTRS)

Trivedi, Kishor S.; Ciardo, Gianfranco; Malhotra, Manish; Sahner, Robin A.

1993-01-01

Several practical issues regarding specifications and solution of dependability and performability models are discussed. Model types with and without rewards are compared. Continuous-time Markov chains (CTMC's) are compared with (continuous-time) Markov reward models (MRM's) and generalized stochastic Petri nets (GSPN's) are compared with stochastic reward nets (SRN's). It is shown that reward-based models could lead to more concise model specifications and solution of a variety of new measures. With respect to the solution of dependability and performability models, three practical issues were identified: largeness, stiffness, and non-exponentiality, and a variety of approaches are discussed to deal with them, including some of the latest research efforts.

Structured, Graphical Analysis of C2 Teams and their Technologies

DTIC Science & Technology

2011-01-01

Two Fratricide Cases Revisited. Paper presented at the 15th International Command and Control Reserach and Technology Symposium (ICCRTS), June 22-24...network-enabled ADF. The paper is thus organized in three sections. The first section introduces the graphics for analyzing the formation and use...summarize, Colored Petri Nets center on networks in which tokens are created, moved, copied, or destroyed (Figure 1). An ellipse denotes a space for

Simulation Modeling of Software Development Processes

NASA Technical Reports Server (NTRS)

Calavaro, G. F.; Basili, V. R.; Iazeolla, G.

1996-01-01

A simulation modeling approach is proposed for the prediction of software process productivity indices, such as cost and time-to-market, and the sensitivity analysis of such indices to changes in the organization parameters and user requirements. The approach uses a timed Petri Net and Object Oriented top-down model specification. Results demonstrate the model representativeness, and its usefulness in verifying process conformance to expectations, and in performing continuous process improvement and optimization.

Scalable Adaptive Architectures for Maritime Operations Center Command and Control

DTIC Science & Technology

2011-05-06

the project to investigate the possibility of using earlier work on the validation and verification of rule bases in addressing the dynamically ...support the organization. To address the dynamically changing rules of engagement of a maritime force as it crosses different geographical areas, GMU... dynamic analysis, makes use of an Occurrence Graph that corresponds to the dynamics (or execution) of the Petri Net, to capture properties

Airport security inspection process model and optimization based on GSPN

NASA Astrophysics Data System (ADS)

Mao, Shuainan

2018-04-01

Aiming at the efficiency of airport security inspection process, Generalized Stochastic Petri Net is used to establish the security inspection process model. The model is used to analyze the bottleneck problem of airport security inspection process. The solution to the bottleneck is given, which can significantly improve the efficiency and reduce the waiting time by adding the place for people to remove their clothes and the X-ray detector.

Optimising the performance of an outpatient setting.

PubMed

Sendi, Pedram; Al, Maiwenn J; Battegay, Manuel; Al Maiwenn, J

2004-01-24

An outpatient setting typically includes experienced and novice resident physicians who are supervised by senior staff physicians. The performance of this kind of outpatient setting, for a given mix of experienced and novice resident physicians, is determined by the number of senior staff physicians available for supervision. The optimum mix of human resources may be determined using discrete-event simulation. An outpatient setting represents a system where concurrency and resource sharing are important. These concepts can be modelled by means of timed Coloured Petri Nets (CPN), which is a discrete-event simulation formalism. We determined the optimum mix of resources (i.e. the number of senior staff physicians needed for a given number of experienced and novice resident physicians) to guarantee efficient overall system performance. In an outpatient setting with 10 resident physicians, two staff physicians are required to guarantee a minimum level of system performance (42-52 patients are seen per 5-hour period). However, with 3 senior staff physicians system performance can be improved substantially (49-56 patients per 5-hour period). An additional fourth staff physician does not substantially enhance system performance (50-57 patients per 5-hour period). Coloured Petri Nets provide a flexible environment in which to simulate an outpatient setting and assess the impact of any staffing changes on overall system performance, to promote informed resource allocation decisions.

Continuous Petri Nets and microRNA analysis in melanoma.

PubMed

Russo, Giulia; Pennisi, Marzio; Boscarino, Roberta; Pappalardo, Francesco

2017-07-31

Personalized target therapies represent one of the possible treatment strategies to fight the ongoing battle against cancer. New treatment interventions are still needed for an effective and successful cancer therapy. In this scenario, we simulated and analyzed the dynamics of BRAF V600E melanoma patients treated with BRAF inhibitors in order to find potentially interesting targets that may make standard treatments more effective in particularly aggressive tumors that may not respond to selective inhibitor drugs. To this aim, we developed a continuous Petri Net model that simulates fundamental signalling cascades involved in melanoma development, such as MAPK and PI3K/AKT, in order to deeply analyze these complex kinase cascades and predict new crucial nodes involved in melanomagenesis. The model pointed out that some microRNAs, like hsa-mir-132, downregulates expression levels of p120RasGAP: under high concentrations of p120RasGAP, MAPK pathway activation is significantly decreased and consequently also PI3K/PDK1/AKT activation. Furthermore, our analysis carried out through the Genomic Data Commons (GDC) Data Portal, shows the evidence that hsa-mir-132 is significantly associated with clinical outcome in melanoma cancer genomic data sets of BRAF-mutated patients. In conclusion, targeting miRNAs through antisense oligonucleotides technology, may suggest the way to enhance the action of of BRAF-inhibitors.

Petri Net computational modelling of Langerhans cell Interferon Regulatory Factor Network predicts their role in T cell activation.

PubMed

Polak, Marta E; Ung, Chuin Ying; Masapust, Joanna; Freeman, Tom C; Ardern-Jones, Michael R

2017-04-06

Langerhans cells (LCs) are able to orchestrate adaptive immune responses in the skin by interpreting the microenvironmental context in which they encounter foreign substances, but the regulatory basis for this has not been established. Utilising systems immunology approaches combining in silico modelling of a reconstructed gene regulatory network (GRN) with in vitro validation of the predictions, we sought to determine the mechanisms of regulation of immune responses in human primary LCs. The key role of Interferon regulatory factors (IRFs) as controllers of the human Langerhans cell response to epidermal cytokines was revealed by whole transcriptome analysis. Applying Boolean logic we assembled a Petri net-based model of the IRF-GRN which provides molecular pathway predictions for the induction of different transcriptional programmes in LCs. In silico simulations performed after model parameterisation with transcription factor expression values predicted that human LC activation of antigen-specific CD8 T cells would be differentially regulated by epidermal cytokine induction of specific IRF-controlled pathways. This was confirmed by in vitro measurement of IFN-γ production by activated T cells. As a proof of concept, this approach shows that stochastic modelling of a specific immune networks renders transcriptome data valuable for the prediction of functional outcomes of immune responses.

Application of Petri Nets in Bone Remodeling

PubMed Central

Li, Lingxi; Yokota, Hiroki

2009-01-01

Understanding a mechanism of bone remodeling is a challenging task for both life scientists and model builders, since this highly interactive and nonlinear process can seldom be grasped by simple intuition. A set of ordinary differential equations (ODEs) have been built for simulating bone formation as well as bone resorption. Although solving ODEs numerically can provide useful predictions for dynamical behaviors in a continuous time frame, an actual bone remodeling process in living tissues is driven by discrete events of molecular and cellular interactions. Thus, an event-driven tool such as Petri nets (PNs), which may dynamically and graphically mimic individual molecular collisions or cellular interactions, seems to augment the existing ODE-based systems analysis. Here, we applied PNs to expand the ODE-based approach and examined discrete, dynamical behaviors of key regulatory molecules and bone cells. PNs have been used in many engineering areas, but their application to biological systems needs to be explored. Our PN model was based on 8 ODEs that described an osteoprotegerin linked molecular pathway consisting of 4 types of bone cells. The models allowed us to conduct both qualitative and quantitative evaluations and evaluate homeostatic equilibrium states. The results support that application of PN models assists understanding of an event-driven bone remodeling mechanism using PN-specific procedures such as places, transitions, and firings. PMID:19838338

Reliability Prediction of Ontology-Based Service Compositions Using Petri Net and Time Series Models

PubMed Central

Li, Jia; Xia, Yunni; Luo, Xin

2014-01-01

OWL-S, one of the most important Semantic Web service ontologies proposed to date, provides a core ontological framework and guidelines for describing the properties and capabilities of their web services in an unambiguous, computer interpretable form. Predicting the reliability of composite service processes specified in OWL-S allows service users to decide whether the process meets the quantitative quality requirement. In this study, we consider the runtime quality of services to be fluctuating and introduce a dynamic framework to predict the runtime reliability of services specified in OWL-S, employing the Non-Markovian stochastic Petri net (NMSPN) and the time series model. The framework includes the following steps: obtaining the historical response times series of individual service components; fitting these series with a autoregressive-moving-average-model (ARMA for short) and predicting the future firing rates of service components; mapping the OWL-S process into a NMSPN model; employing the predicted firing rates as the model input of NMSPN and calculating the normal completion probability as the reliability estimate. In the case study, a comparison between the static model and our approach based on experimental data is presented and it is shown that our approach achieves higher prediction accuracy. PMID:24688429

Petri net-based dependability modeling methodology for reconfigurable field programmable gate arrays

NASA Astrophysics Data System (ADS)

Graczyk, Rafał; Orleański, Piotr; Poźniak, Krzysztof

2015-09-01

Dependability modeling is an important issue for aerospace and space equipment designers. From system level perspective, one has to choose from multitude of possible architectures, redundancy levels, component combinations in a way to meet desired properties and dependability and finally fit within required cost and time budgets. Modeling of such systems is getting harder as its levels of complexity grow together with demand for more functional and flexible, yet more available systems that govern more and more crucial parts of our civilization's infrastructure (aerospace transport systems, telecommunications, exploration probes). In this article promising method of modeling complex systems using Petri networks is introduced in context of qualitative and quantitative dependability analysis. This method, although with some limitation and drawback offer still convenient visual formal method of describing system behavior on different levels (functional, timing, random events) and offers straight correspondence to underlying mathematical engine, perfect for simulations and engineering support.

Improvement on `structure of weakly 2-dependent siphons'

NASA Astrophysics Data System (ADS)

Chao, Daniel Y.

2015-01-01

Li and Zhou propose simpler Petri net controllers based on the concept of elementary siphons (generally much smaller than the set of all strict minimum siphons (SMSs) in large Petri nets) to minimise the addition of control places. SMSs can be divided into two groups: elementary and dependant; characteristic T-vectors of the latter are linear combinations of that of the former. A T-vector η is associated with each siphon S such that η(i) is the number of tokens gained in or lost from S by firing transition ti once. A dependent siphon S0 strongly depends on elementary siphons S1, S2, … , Sk if η0 = a1η1 + a2η2 + ṡṡṡ + akηk with all ai (i = 1, 2, 3, … , k) positive. S0 is a weakly dependent siphon if some ai is negative. The T-vectors (resp. number) for elementary siphons are mutually independent (linear to the size of the net). In an earlier paper, we show that there exists a third siphon S3 such that ηβ = η1 + η2 - η3. This equation (called η relationship) plays an important role for optimal control of weakly dependent siphons. However, it assumes that all above S span between exactly two processes. For a well-known benchmark, however, most dependent siphons span more than two processes. This paper improves by removing this restriction and shows that ηβ = η1 + η2 - η3 holds as long as S1∩S2 is another emptiable siphon.

Conception of discrete systems decomposition algorithm using p-invariants and hypergraphs

NASA Astrophysics Data System (ADS)

Stefanowicz, Ł.

2016-09-01

In the article author presents an idea of decomposition algorithm of discrete systems described by Petri Nets using pinvariants. Decomposition process is significant from the point of view of discrete systems design, because it allows separation of the smaller sequential parts. Proposed algorithm uses modified Martinez-Silva method as well as author's selection algorithm. The developed method is a good complement of classical decomposition algorithms using graphs and hypergraphs.

Some remarks on quantum physics, stochastic processes, and nonlinear filtering theory

NASA Astrophysics Data System (ADS)

Balaji, Bhashyam

2016-05-01

The mathematical similarities between quantum mechanics and stochastic processes has been studied in the literature. Some of the major results are reviewed, such as the relationship between the Fokker-Planck equation and the Schrödinger equation. Also reviewed are more recent results that show the mathematical similarities between quantum many particle systems and concepts in other areas of applied science, such as stochastic Petri nets. Some connections to filtering theory are discussed.

Petri Nets with Fuzzy Logic (PNFL): Reverse Engineering and Parametrization

PubMed Central

Küffner, Robert; Petri, Tobias; Windhager, Lukas; Zimmer, Ralf

2010-01-01

Background The recent DREAM4 blind assessment provided a particularly realistic and challenging setting for network reverse engineering methods. The in silico part of DREAM4 solicited the inference of cycle-rich gene regulatory networks from heterogeneous, noisy expression data including time courses as well as knockout, knockdown and multifactorial perturbations. Methodology and Principal Findings We inferred and parametrized simulation models based on Petri Nets with Fuzzy Logic (PNFL). This completely automated approach correctly reconstructed networks with cycles as well as oscillating network motifs. PNFL was evaluated as the best performer on DREAM4 in silico networks of size 10 with an area under the precision-recall curve (AUPR) of 81%. Besides topology, we inferred a range of additional mechanistic details with good reliability, e.g. distinguishing activation from inhibition as well as dependent from independent regulation. Our models also performed well on new experimental conditions such as double knockout mutations that were not included in the provided datasets. Conclusions The inference of biological networks substantially benefits from methods that are expressive enough to deal with diverse datasets in a unified way. At the same time, overly complex approaches could generate multiple different models that explain the data equally well. PNFL appears to strike the balance between expressive power and complexity. This also applies to the intuitive representation of PNFL models combining a straightforward graphical notation with colloquial fuzzy parameters. PMID:20862218

Modelling of Safety Instrumented Systems by using Bernoulli trials: towards the notion of odds on for SIS failures analysis

NASA Astrophysics Data System (ADS)

Cauffriez, Laurent

2017-01-01

This paper deals with the modeling of a random failures process of a Safety Instrumented System (SIS). It aims to identify the expected number of failures for a SIS during its lifecycle. Indeed, the fact that the SIS is a system being tested periodically gives the idea to apply Bernoulli trials to characterize the random failure process of a SIS and thus to verify if the PFD (Probability of Failing Dangerously) experimentally obtained agrees with the theoretical one. Moreover, the notion of "odds on" found in Bernoulli theory allows engineers and scientists determining easily the ratio between “outcomes with success: failure of SIS” and “outcomes with unsuccess: no failure of SIS” and to confirm that SIS failures occur sporadically. A Stochastic P-temporised Petri net is proposed and serves as a reference model for describing the failure process of a 1oo1 SIS architecture. Simulations of this stochastic Petri net demonstrate that, during its lifecycle, the SIS is rarely in a state in which it cannot perform its mission. Experimental results are compared to Bernoulli trials in order to validate the powerfulness of Bernoulli trials for the modeling of the failures process of a SIS. The determination of the expected number of failures for a SIS during its lifecycle opens interesting research perspectives for engineers and scientists by completing the notion of PFD.

Comparing digraph and Petri net approaches to deadlock avoidance in FMS.

PubMed

Fanti, M P; Maione, B; Turchiano, B

2000-01-01

Flexible manufacturing systems (FMSs) are modern production facilities with easy adaptability to variable production plans and goals. These systems may exhibit deadlock situations occurring when a circular wait arises because each piece in a set requires a resource currently held by another job in the same set. Several authors have proposed different policies to control resource allocation in order to avoid deadlock problems. These approaches are mainly based on some formal models of manufacturing systems, such as Petri nets (PNs), directed graphs, etc. Since they describe various peculiarities of the FMS operation in a modular and systematic way, PNs are the most extensively used tool to model such systems. On the other hand, digraphs are more synthetic than PNs because their vertices are just the system resources. So, digraphs describe the interactions between jobs and resources only, while neglecting other details on the system operation. The aim of this paper is to show the tight connections between the two approaches to the deadlock problem, by proposing a unitary framework that links graph-theoretic and PN models and results. In this context, we establish a direct correspondence between the structural elements of the PN (empty siphons) and those of the digraphs (maximal-weight zero-outdegree strong components) characterizing a deadlock occurrence. The paper also shows that the avoidance policies derived from digraphs can be implemented by controlled PNs.

Parallelizing Timed Petri Net simulations

NASA Technical Reports Server (NTRS)

Nicol, David M.

1993-01-01

The possibility of using parallel processing to accelerate the simulation of Timed Petri Nets (TPN's) was studied. It was recognized that complex system development tools often transform system descriptions into TPN's or TPN-like models, which are then simulated to obtain information about system behavior. Viewed this way, it was important that the parallelization of TPN's be as automatic as possible, to admit the possibility of the parallelization being embedded in the system design tool. Later years of the grant were devoted to examining the problem of joint performance and reliability analysis, to explore whether both types of analysis could be accomplished within a single framework. In this final report, the results of our studies are summarized. We believe that the problem of parallelizing TPN's automatically for MIMD architectures has been almost completely solved for a large and important class of problems. Our initial investigations into joint performance/reliability analysis are two-fold; it was shown that Monte Carlo simulation, with importance sampling, offers promise of joint analysis in the context of a single tool, and methods for the parallel simulation of general Continuous Time Markov Chains, a model framework within which joint performance/reliability models can be cast, were developed. However, very much more work is needed to determine the scope and generality of these approaches. The results obtained in our two studies, future directions for this type of work, and a list of publications are included.

Controllability of control and mixture weakly dependent siphons in S3PR

NASA Astrophysics Data System (ADS)

Hong, Liang; Chao, Daniel Y.

2013-08-01

Deadlocks in a flexible manufacturing system modelled by Petri nets arise from insufficiently marked siphons. Monitors are added to control these siphons to avoid deadlocks rendering the system too complicated since the total number of monitors grows exponentially. Li and Zhou propose to add monitors only to elementary siphons while controlling the other (strongly or weakly) dependent siphons by adjusting control depth variables. To avoid generating new siphons, the control arcs are ended at source transitions of process nets. This disturbs the original model more and hence loses more live states. Negative terms in the controllability make the control policy for weakly dependent siphons rather conservative. We studied earlier on the controllability of strongly dependent siphons and proposed to add monitors in the order of basic, compound, control, partial mixture and full mixture (strongly dependent) siphons to reduce the number of mixed integer programming iterations and redundant monitors. This article further investigates the controllability of siphons derived from weakly 2-compound siphons. We discover that the controllability for weakly and strongly compound siphons is similar. It no longer holds for control and mixture siphons. Some control and mixture siphons, derived from strongly 2-compound siphons are not redundant - no longer so for those derived from weakly 2-compound siphons; that is all control and mixture siphons are redundant. They do not need to be the conservative one as proposed by Li and Zhou. Thus, we can adopt the maximally permissive control policy even though new siphons are generated.

Modeling and analysis of equipment managers in manufacturing execution systems for semiconductor packaging.

PubMed

Cheng, F T; Yang, H C; Luo, T L; Feng, C; Jeng, M

2000-01-01

Equipment Managers (EMs) play a major role in a Manufacturing Execution System (MES). They serve as the communication bridge between the components of an MES and the equipment. The purpose of this paper is to propose a novel methodology for developing analytical and simulation models for the EM such that the validity and performance of the EM can be evaluated. Domain knowledge and requirements are collected from a real semiconductor packaging factory. By using IDEFO and state diagrams, a static functional model and a dynamic state model of the EM are built. Next, these two models are translated into a Petri net model. This allows qualitative and quantitative analyses of the system. The EM net model is then expanded into the MES net model. Therefore, the performance of an EM in the MES environment can be evaluated. These evaluation results are good references for design and decision making.

Estimation and enhancement of real-time software reliability through mutation analysis

NASA Technical Reports Server (NTRS)

Geist, Robert; Offutt, A. J.; Harris, Frederick C., Jr.

1992-01-01

A simulation-based technique for obtaining numerical estimates of the reliability of N-version, real-time software is presented. An extended stochastic Petri net is employed to represent the synchronization structure of N versions of the software, where dependencies among versions are modeled through correlated sampling of module execution times. Test results utilizing specifications for NASA's planetary lander control software indicate that mutation-based testing could hold greater potential for enhancing reliability than the desirable but perhaps unachievable goal of independence among N versions.

UML activity diagram swimlanes in logic controller design

NASA Astrophysics Data System (ADS)

Grobelny, Michał; Grobelna, Iwona

2015-12-01

Logic controller behavior can be specified using various techniques, including UML activity diagrams and control Petri nets. Each technique has its advantages and disadvantages. Application of both specification types in one project allows to take benefits from both of them. Additional elements of UML models make it possible to divide a specification into some parts, considered from other point of view (logic controller, user or system). The paper introduces an idea to use UML activity diagrams with swimlanes to increase the understandability of design models.

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram.

PubMed

Li, Chen; Nagasaki, Masao; Saito, Ayumu; Miyano, Satoru

2010-04-01

With an accumulation of in silico data obtained by simulating large-scale biological networks, a new interest of research is emerging for elucidating how living organism functions over time in cells. Investigating the dynamic features of current computational models promises a deeper understanding of complex cellular processes. This leads us to develop a method that utilizes structural properties of the model over all simulation time steps. Further, user-friendly overviews of dynamic behaviors can be considered to provide a great help in understanding the variations of system mechanisms. We propose a novel method for constructing and analyzing a so-called active state transition diagram (ASTD) by using time-course simulation data of a high-level Petri net. Our method includes two new algorithms. The first algorithm extracts a series of subnets (called temporal subnets) reflecting biological components contributing to the dynamics, while retaining positive mathematical qualities. The second one creates an ASTD composed of unique temporal subnets. ASTD provides users with concise information allowing them to grasp and trace how a key regulatory subnet and/or a network changes with time. The applicability of our method is demonstrated by the analysis of the underlying model for circadian rhythms in Drosophila. Building ASTD is a useful means to convert a hybrid model dealing with discrete, continuous and more complicated events to finite time-dependent states. Based on ASTD, various analytical approaches can be applied to obtain new insights into not only systematic mechanisms but also dynamics.

Short-term scheduling of crude oil operations in refinery with high-fusion-point oil and two transportation pipelines

NASA Astrophysics Data System (ADS)

Wu, NaiQi; Zhu, MengChu; Bai, LiPing; Li, ZhiWu

2016-07-01

In some refineries, storage tanks are located at two different sites, one for low-fusion-point crude oil and the other for high one. Two pipelines are used to transport different oil types. Due to the constraints resulting from the high-fusion-point oil transportation, it is challenging to schedule such a system. This work studies the scheduling problem from a control-theoretic perspective. It proposes to use a hybrid Petri net method to model the system. It then finds the schedulability conditions by analysing the dynamic behaviour of the net model. Next, it proposes an efficient scheduling method to minimize the cost of high-fusion-point oil transportation. Finally, it gives a complex industrial case study to show its application.

Event Detection for Hydrothermal Plumes: A case study at Grotto Vent

NASA Astrophysics Data System (ADS)

Bemis, K. G.; Ozer, S.; Xu, G.; Rona, P. A.; Silver, D.

2012-12-01

Evidence is mounting that geologic events such as volcanic eruptions (and intrusions) and earthquakes (near and far) influence the flow rates and temperatures of hydrothermal systems. Connecting such suppositions to observations of hydrothermal output is challenging, but new ongoing time series have the potential to capture such events. This study explores using activity detection, a technique modified from computer vision, to identify pre-defined events within an extended time series recorded by COVIS (Cabled Observatory Vent Imaging Sonar) and applies it to a time series, with gaps, from Sept 2010 to the present; available measurements include plume orientation, plume rise rate, and diffuse flow area at the NEPTUNE Canada Observatory at Grotto Vent, Main Endeavour Field, Juan de Fuca Ridge. Activity detection is the process of finding a pattern (activity) in a data set containing many different types of patterns. Among many approaches proposed to model and detect activities, we have chosen a graph-based technique, Petri Nets, as they do not require training data to model the activity. They use the domain expert's knowledge to build the activity as a combination of feature states and their transitions (actions). Starting from a conceptual model of how hydrothermal plumes respond to daily tides, we have developed a Petri Net based detection algorithm that identifies deviations from the specified response. Initially we assumed that the orientation of the plume would change smoothly and symmetrically in a consistent daily pattern. However, results indicate that the rate of directional changes varies. The present Petri Net detects unusually large and rapid changes in direction or amount of bending; however inspection of Figure 1 suggests that many of the events detected may be artifacts resulting from gaps in the data or from the large temporal spacing. Still, considerable complexity overlies the "normal" tidal response pattern (the data has a dominant frequency of ~12.9 hours). We are in the process of defining several events of particular scientific interest: 1) transient behavioral changes associated with atmospheric storms, earthquakes or volcanic intrusions or eruptions, 2) mutual interaction of neighboring plumes on each other's behavior, and 3) rapid shifts in plume direction that indicate the presence of unusual currents or changes in currents. We will query the existing data to see if these relationships are ever observed as well as testing our understanding of the "normal" pattern of response to tidal currents.Figure 1. Arrows indicate plume orientation at a given time (time axis in days after 9/29/10) and stars indicate times when orientation changes rapidly.

Modeling and optimum time performance for concurrent processing

NASA Technical Reports Server (NTRS)

Mielke, Roland R.; Stoughton, John W.; Som, Sukhamoy

1988-01-01

The development of a new graph theoretic model for describing the relation between a decomposed algorithm and its execution in a data flow environment is presented. Called ATAMM, the model consists of a set of Petri net marked graphs useful for representing decision-free algorithms having large-grained, computationally complex primitive operations. Performance time measures which determine computing speed and throughput capacity are defined, and the ATAMM model is used to develop lower bounds for these times. A concurrent processing operating strategy for achieving optimum time performance is presented and illustrated by example.

The development of advanced manufacturing systems

NASA Astrophysics Data System (ADS)

Doumeingts, Guy; Vallespir, Bruno; Darricau, Didier; Roboam, Michel

Various methods for the design of advanced manufacturing systems (AMSs) are reviewed. The specifications for AMSs and problems inherent in their development are first discussed. Three models, the Computer Aided Manufacturing-International model, the National Bureau of Standards model, and the GRAI model, are considered in detail. Hierarchical modeling tools such as structured analysis and design techniques, Petri nets, and the Icam definition method are used in the development of integrated manufacturing models. Finally, the GRAI method is demonstrated in the design of specifications for the production management system of the Snecma AMS.

Sociophysics of sexism: normal and anomalous petrie multipliers

NASA Astrophysics Data System (ADS)

Eliazar, Iddo

2015-07-01

A recent mathematical model by Karen Petrie explains how sexism towards women can arise in organizations where male and female are equally sexist. Indeed, the Petrie model predicts that such sexism will emerge whenever there is a male majority, and quantifies this majority bias by the ‘Petrie multiplier’: the square of the male/female ratio. In this paper—emulating the shift from ‘normal’ to ‘anomalous’ diffusion—we generalize the Petrie model to a stochastic Poisson model that accommodates heterogeneously sexist men and woman, and that extends the ‘normal’ quadratic Petrie multiplier to ‘anomalous’ non-quadratic multipliers. The Petrie multipliers span a full spectrum of behaviors which we classify into four universal types. A variation of the stochastic Poisson model and its Petrie multipliers is further applied to the context of cyber warfare.

Systematic reconstruction of TRANSPATH data into Cell System Markup Language

PubMed Central

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-01-01

Background Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. Results We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. Conclusion By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions. PMID:18570683

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma

PubMed Central

Naz, Anam; Obaid, Ayesha; Awan, Faryal M.; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells. PMID:28932213

Genomic data assimilation for estimating hybrid functional Petri net from time-course gene expression data.

PubMed

Nagasaki, Masao; Yamaguchi, Rui; Yoshida, Ryo; Imoto, Seiya; Doi, Atsushi; Tamada, Yoshinori; Matsuno, Hiroshi; Miyano, Satoru; Higuchi, Tomoyuki

2006-01-01

We propose an automatic construction method of the hybrid functional Petri net as a simulation model of biological pathways. The problems we consider are how we choose the values of parameters and how we set the network structure. Usually, we tune these unknown factors empirically so that the simulation results are consistent with biological knowledge. Obviously, this approach has the limitation in the size of network of interest. To extend the capability of the simulation model, we propose the use of data assimilation approach that was originally established in the field of geophysical simulation science. We provide genomic data assimilation framework that establishes a link between our simulation model and observed data like microarray gene expression data by using a nonlinear state space model. A key idea of our genomic data assimilation is that the unknown parameters in simulation model are converted as the parameter of the state space model and the estimates are obtained as the maximum a posteriori estimators. In the parameter estimation process, the simulation model is used to generate the system model in the state space model. Such a formulation enables us to handle both the model construction and the parameter tuning within a framework of the Bayesian statistical inferences. In particular, the Bayesian approach provides us a way of controlling overfitting during the parameter estimations that is essential for constructing a reliable biological pathway. We demonstrate the effectiveness of our approach using synthetic data. As a result, parameter estimation using genomic data assimilation works very well and the network structure is suitably selected.

Time-dependent structural transformation analysis to high-level Petri net model with active state transition diagram

PubMed Central

2010-01-01

Background With an accumulation of in silico data obtained by simulating large-scale biological networks, a new interest of research is emerging for elucidating how living organism functions over time in cells. Investigating the dynamic features of current computational models promises a deeper understanding of complex cellular processes. This leads us to develop a method that utilizes structural properties of the model over all simulation time steps. Further, user-friendly overviews of dynamic behaviors can be considered to provide a great help in understanding the variations of system mechanisms. Results We propose a novel method for constructing and analyzing a so-called active state transition diagram (ASTD) by using time-course simulation data of a high-level Petri net. Our method includes two new algorithms. The first algorithm extracts a series of subnets (called temporal subnets) reflecting biological components contributing to the dynamics, while retaining positive mathematical qualities. The second one creates an ASTD composed of unique temporal subnets. ASTD provides users with concise information allowing them to grasp and trace how a key regulatory subnet and/or a network changes with time. The applicability of our method is demonstrated by the analysis of the underlying model for circadian rhythms in Drosophila. Conclusions Building ASTD is a useful means to convert a hybrid model dealing with discrete, continuous and more complicated events to finite time-dependent states. Based on ASTD, various analytical approaches can be applied to obtain new insights into not only systematic mechanisms but also dynamics. PMID:20356411

An enhanced Petri-net model to predict synergistic effects of pairwise drug combinations from gene microarray data.

PubMed

Jin, Guangxu; Zhao, Hong; Zhou, Xiaobo; Wong, Stephen T C

2011-07-01

Prediction of synergistic effects of drug combinations has traditionally been relied on phenotypic response data. However, such methods cannot be used to identify molecular signaling mechanisms of synergistic drug combinations. In this article, we propose an enhanced Petri-Net (EPN) model to recognize the synergistic effects of drug combinations from the molecular response profiles, i.e. drug-treated microarray data. We addressed the downstream signaling network of the targets for the two individual drugs used in the pairwise combinations and applied EPN to the identified targeted signaling network. In EPN, drugs and signaling molecules are assigned to different types of places, while drug doses and molecular expressions are denoted by color tokens. The changes of molecular expressions caused by treatments of drugs are simulated by two actions of EPN: firing and blasting. Firing is to transit the drug and molecule tokens from one node or place to another, and blasting is to reduce the number of molecule tokens by drug tokens in a molecule node. The goal of EPN is to mediate the state characterized by control condition without any treatment to that of treatment and to depict the drug effects on molecules by the drug tokens. We applied EPN to our generated pairwise drug combination microarray data. The synergistic predictions using EPN are consistent with those predicted using phenotypic response data. The molecules responsible for the synergistic effects with their associated feedback loops display the mechanisms of synergism. The software implemented in Python 2.7 programming language is available from request. stwong@tmhs.org.

Petri Net-Based Model of Helicobacter pylori Mediated Disruption of Tight Junction Proteins in Stomach Lining during Gastric Carcinoma.

PubMed

Naz, Anam; Obaid, Ayesha; Awan, Faryal M; Ikram, Aqsa; Ahmad, Jamil; Ali, Amjad

2017-01-01

Tight junctions help prevent the passage of digestive enzymes and microorganisms through the space between adjacent epithelial cells lining. However, Helicobacter pylori encoded virulence factors negatively regulate these tight junctions and contribute to dysfunction of gastric mucosa. Here, we have predicted the regulation of important tight junction proteins, such as Zonula occludens-1, Claudin-2 and Connexin32 in the presence of pathogenic proteins. Molecular events such as post translational modifications and crosstalk between phosphorylation, O-glycosylation, palmitoylation and methylation are explored which may compromise the integrity of these tight junction proteins. Furthermore, the signaling pathways disrupted by dysregulated kinases, proteins and post-translational modifications are reviewed to design an abstracted computational model showing the situation-dependent dynamic behaviors of these biological processes and entities. A qualitative hybrid Petri Net model is therefore constructed showing the altered host pathways in the presence of virulence factor cytotoxin-associated gene A, leading to the disruption of tight junction proteins. The model is qualitative logic-based, which does not depend on any kinetic parameter and quantitative data and depends on knowledge derived from experiments. The designed model provides insights into the tight junction disruption and disease progression. Model is then verified by the available experimental data, nevertheless formal in vitro experimentation is a promising way to ensure its validation. The major findings propose that H. pylori activated kinases are responsible to trigger specific post translational modifications within tight junction proteins, at specific sites. These modifications may favor alterations in gastric barrier and provide a route to bacterial invasion into host cells.

Systematic reconstruction of TRANSPATH data into cell system markup language.

PubMed

Nagasaki, Masao; Saito, Ayumu; Li, Chen; Jeong, Euna; Miyano, Satoru

2008-06-23

Many biological repositories store information based on experimental study of the biological processes within a cell, such as protein-protein interactions, metabolic pathways, signal transduction pathways, or regulations of transcription factors and miRNA. Unfortunately, it is difficult to directly use such information when generating simulation-based models. Thus, modeling rules for encoding biological knowledge into system-dynamics-oriented standardized formats would be very useful for fully understanding cellular dynamics at the system level. We selected the TRANSPATH database, a manually curated high-quality pathway database, which provides a plentiful source of cellular events in humans, mice, and rats, collected from over 31,500 publications. In this work, we have developed 16 modeling rules based on hybrid functional Petri net with extension (HFPNe), which is suitable for graphical representing and simulating biological processes. In the modeling rules, each Petri net element is incorporated with Cell System Ontology to enable semantic interoperability of models. As a formal ontology for biological pathway modeling with dynamics, CSO also defines biological terminology and corresponding icons. By combining HFPNe with the CSO features, it is possible to make TRANSPATH data to simulation-based and semantically valid models. The results are encoded into a biological pathway format, Cell System Markup Language (CSML), which eases the exchange and integration of biological data and models. By using the 16 modeling rules, 97% of the reactions in TRANSPATH are converted into simulation-based models represented in CSML. This reconstruction demonstrates that it is possible to use our rules to generate quantitative models from static pathway descriptions.

75 FR 65363 - Basic Behavioral and Social Science Opportunity Network (OppNet)

Federal Register 2010, 2011, 2012, 2013, 2014

2010-10-22

... public meeting to promote and publicize the Basic Behavioral and Social Science Opportunity Network (Opp... . Background: The Basic Behavioral and Social Science Opportunity Network (OppNet) is a trans-NIH initiative to expand the agency's funding of basic behavioral and social sciences research (b-BSSR). OppNet prioritizes...

Evaluation of sunlight-exposed pyrethroid-treated netting for the control of face fly and housefly (Diptera: Muscidae).

PubMed

Peck, George W; Ferguson, Holly J; LePage, Jane T; Hebert, Vincent R; O'Neal, Sally D; Walsh, Douglas B

2014-01-01

Face flies, Musca autumnalis De Geer (Diptera: Muscidae), and houseflies, Musca domestica L. (Diptera: Muscidae), have a significant impact on livestock and dairy production throughout North America. Pyrethroid insecticide efficacy can be affected by exposure to direct sunlight, and the rate of photodegradation is substrate and formulation dependent. Insecticide-treated netting (ITN) is finding new applications in crop and livestock production systems. A baseline study using long-duration no-choice assays has been carried out to gauge the effectiveness of ITN treated with β-cyfluthrin, λ-cyhalothrin and bifenthrin on face flies and houseflies. After 12 weeks in direct sunlight, ITN treated with β-cyfluthrin was still highly insecticidal to face flies and houseflies, producing 100% mortality in petri dish assays. However, sunlight reduced the insecticidal activity of λ-cyhalothrin, with 3% of face flies and 50% of houseflies surviving after exposure to ITN that had been deployed for 10 weeks. Insecticidal activity was greatly reduced on bifenthrin-treated netting, with 20% of face flies and 50% of houseflies surviving in assays with netting deployed for only 3 weeks. With careful choice of the pyrethroid applied, treated netting could be an important component of livestock integrated pest management programs focused on sustainable practices. © 2013 Society of Chemical Industry.

Characterizing parameters of Jatropha curcas cell cultures for microgravity studies

NASA Astrophysics Data System (ADS)

Vendrame, Wagner A.; Pinares, Ania

2013-06-01

Jatropha (Jatropha curcas) is a tropical perennial species identified as a potential biofuel crop. The oil is of excellent quality and it has been successfully tested as biodiesel and in jet fuel mixes. However, studies on breeding and genetic improvement of jatropha are limited. Space offers a unique environment for experiments aiming at the assessment of mutations and differential gene expression of crops and in vitro cultures of plants are convenient for studies of genetic variation as affected by microgravity. However, before microgravity studies can be successfully performed, pre-flight experiments are necessary to characterize plant material and validate flight hardware environmental conditions. Such preliminary studies set the ground for subsequent spaceflight experiments. The objectives of this study were to compare the in vitro growth of cultures from three explant sources (cotyledon, leaf, and stem sections) of three jatropha accessions (Brazil, India, and Tanzania) outside and inside the petriGAP, a modified group activation pack (GAP) flight hardware to fit petri dishes. In vitro jatropha cell cultures were established in petri dishes containing a modified MS medium and maintained in a plant growth chamber at 25 ± 2 °C in the dark. Parameters evaluated were surface area of the explant tissue (A), fresh weight (FW), and dry weight (DW) for a period of 12 weeks. Growth was observed for cultures from all accessions at week 12, including subsequent plantlet regeneration. For all accessions differences in A, FW and DW were observed for inside vs. outside the PetriGAPs. Growth parameters were affected by accession (genotype), explant type, and environment. The type of explant influenced the type of cell growth and subsequent plantlet regeneration capacity. However, overall cell growth showed no abnormalities. The present study demonstrated that jatropha in vitro cell cultures are suitable for growth inside PetriGAPs for a period of 12 weeks. The parameters evaluated in this study provide the basic ground work and pre-flight assessment needed to justify a model for microgravity studies with jatropha in vitro cell cultures. Future studies should focus on results of experiments performed with jatropha in vitro cultures in microgravity.

Design for Maintainability with Modified Petri Nets (MPNs): Shipboard Propulsion System Application.

DTIC Science & Technology

1984-11-01

hazard (in acco- Fance with current environmental protection requirements). P20 YES T20 T2 1 EOOW report to 000, "Fire hazards removed from No engine room...8217-..! AARCA: GAS TURBINE MAIN ENGINE - GENERATOR Room NO 2 , .’ .- " SE7 NO. 2 \\ N 2 GEN MRGA GTM ,RZT 4o i .. .E rAF- _....Pr AJ*~ IAMR...GA Z0GYM GEN "-- ~ ~ P LL-L GIM. I I - GT MAIN ENGINE/ \\ t I . ROOM NO. I GAS 7RBINE ALIX MCHRY AUX MCHRY O OROO NO OOM NO. GENEU.ATOF ROOM NO 2 R

Temporal logics and real time expert systems.

PubMed

Blom, J A

1996-10-01

This paper introduces temporal logics. Due to the eternal compromise between expressive adequacy and reasoning efficiency that must decided upon in any application, full (first order logic or modal logic based) temporal logics are frequently not suitable. This is especially true in real time expert systems, where a fixed (and usually small) response time must be guaranteed. One such expert system, Fagan's VM, is reviewed, and a delineation is given of how to formally describe and reason with time in medical protocols. It is shown that Petri net theory is a useful tool to check the correctness of formalised protocols.

Hierarchical analytical and simulation modelling of human-machine systems with interference

NASA Astrophysics Data System (ADS)

Braginsky, M. Ya; Tarakanov, D. V.; Tsapko, S. G.; Tsapko, I. V.; Baglaeva, E. A.

2017-01-01

The article considers the principles of building the analytical and simulation model of the human operator and the industrial control system hardware and software. E-networks as the extension of Petri nets are used as the mathematical apparatus. This approach allows simulating complex parallel distributed processes in human-machine systems. The structural and hierarchical approach is used as the building method for the mathematical model of the human operator. The upper level of the human operator is represented by the logical dynamic model of decision making based on E-networks. The lower level reflects psychophysiological characteristics of the human-operator.

ATAMM enhancement and multiprocessing performance evaluation

NASA Technical Reports Server (NTRS)

Stoughton, John W.

1994-01-01

The algorithm to architecture mapping model (ATAAM) is a Petri net based model which provides a strategy for periodic execution of a class of real-time algorithms on multicomputer dataflow architecture. The execution of large-grained, decision-free algorithms on homogeneous processing elements is studied. The ATAAM provides an analytical basis for calculating performance bounds on throughput characteristics. Extension of the ATAMM as a strategy for cyclo-static scheduling provides for a truly distributed ATAMM multicomputer operating system. An ATAAM testbed consisting of a centralized graph manager and three processors is described using embedded firmware on 68HC11 microcontrollers.

Resource conflict detection and removal strategy for nondeterministic emergency response processes using Petri nets

NASA Astrophysics Data System (ADS)

Zeng, Qingtian; Liu, Cong; Duan, Hua

2016-09-01

Correctness of an emergency response process specification is critical to emergency mission success. Therefore, errors in the specification should be detected and corrected at build-time. In this paper, we propose a resource conflict detection approach and removal strategy for emergency response processes constrained by resources and time. In this kind of emergency response process, there are two timing functions representing the minimum and maximum execution time for each activity, respectively, and many activities require resources to be executed. Based on the RT_ERP_Net, the earliest time to start each activity and the ideal execution time of the process can be obtained. To detect and remove the resource conflicts in the process, the conflict detection algorithms and a priority-activity-first resolution strategy are given. In this way, real execution time for each activity is obtained and a conflict-free RT_ERP_Net is constructed by adding virtual activities. By experiments, it is proved that the resolution strategy proposed can shorten the execution time of the whole process to a great degree.

Modelling of different enzyme productions by solid-state fermentation on several agro-industrial residues.

PubMed

Diaz, Ana Belen; Blandino, Ana; Webb, Colin; Caro, Ildefonso

2016-11-01

A simple kinetic model, with only three fitting parameters, for several enzyme productions in Petri dishes by solid-state fermentation is proposed in this paper, which may be a valuable tool for simulation of this type of processes. Basically, the model is able to predict temporal fungal enzyme production by solid-state fermentation on complex substrates, maximum enzyme activity expected and time at which these maxima are reached. In this work, several fermentations in solid state were performed in Petri dishes, using four filamentous fungi grown on different agro-industrial residues, measuring xylanase, exo-polygalacturonase, cellulose and laccase activities over time. Regression coefficients after fitting experimental data to the proposed model turned out to be quite high in all cases. In fact, these results are very interesting considering, on the one hand, the simplicity of the model and, on the other hand, that enzyme activities correspond to different enzymes, produced by different fungi on different substrates.

Online model checking approach based parameter estimation to a neuronal fate decision simulation model in Caenorhabditis elegans with hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Koh, Chuan Hock; Miyano, Satoru

2011-05-01

Mathematical modeling and simulation studies are playing an increasingly important role in helping researchers elucidate how living organisms function in cells. In systems biology, researchers typically tune many parameters manually to achieve simulation results that are consistent with biological knowledge. This severely limits the size and complexity of simulation models built. In order to break this limitation, we propose a computational framework to automatically estimate kinetic parameters for a given network structure. We utilized an online (on-the-fly) model checking technique (which saves resources compared to the offline approach), with a quantitative modeling and simulation architecture named hybrid functional Petri net with extension (HFPNe). We demonstrate the applicability of this framework by the analysis of the underlying model for the neuronal cell fate decision model (ASE fate model) in Caenorhabditis elegans. First, we built a quantitative ASE fate model containing 3327 components emulating nine genetic conditions. Then, using our developed efficient online model checker, MIRACH 1.0, together with parameter estimation, we ran 20-million simulation runs, and were able to locate 57 parameter sets for 23 parameters in the model that are consistent with 45 biological rules extracted from published biological articles without much manual intervention. To evaluate the robustness of these 57 parameter sets, we run another 20 million simulation runs using different magnitudes of noise. Our simulation results concluded that among these models, one model is the most reasonable and robust simulation model owing to the high stability against these stochastic noises. Our simulation results provide interesting biological findings which could be used for future wet-lab experiments.

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling.

PubMed

Jacobsen, Annika; Heijmans, Nika; Verkaar, Folkert; Smit, Martine J; Heringa, Jaap; van Amerongen, Renée; Feenstra, K Anton

2016-01-01

The Wnt/β-catenin signaling pathway is important for multiple developmental processes and tissue maintenance in adults. Consequently, deregulated signaling is involved in a range of human diseases including cancer and developmental defects. A better understanding of the intricate regulatory mechanism and effect of physiological (active) and pathophysiological (hyperactive) WNT signaling is important for predicting treatment response and developing novel therapies. The constitutively expressed CTNNB1 (commonly and hereafter referred to as β-catenin) is degraded by a destruction complex, composed of amongst others AXIN1 and GSK3. The destruction complex is inhibited during active WNT signaling, leading to β-catenin stabilization and induction of β-catenin/TCF target genes. In this study we investigated the mechanism and effect of β-catenin stabilization during active and hyperactive WNT signaling in a combined in silico and in vitro approach. We constructed a Petri net model of Wnt/β-catenin signaling including main players from the plasma membrane (WNT ligands and receptors), cytoplasmic effectors and the downstream negative feedback target gene AXIN2. We validated that our model can be used to simulate both active (WNT stimulation) and hyperactive (GSK3 inhibition) signaling by comparing our simulation and experimental data. We used this experimentally validated model to get further insights into the effect of the negative feedback regulator AXIN2 upon WNT stimulation and observed an attenuated β-catenin stabilization. We furthermore simulated the effect of APC inactivating mutations, yielding a stabilization of β-catenin levels comparable to the Wnt-pathway activities observed in colorectal and breast cancer. Our model can be used for further investigation and viable predictions of the role of Wnt/β-catenin signaling in oncogenesis and development.

Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis

PubMed Central

Formanowicz, Dorota; Radom, Marcin; Zawierucha, Piotr; Formanowicz, Piotr

2017-01-01

The functioning of both normal and pathological tissues depends on an adequate supply of oxygen through the blood vessels. A process called angiogenesis, in which new endothelial cells and smooth muscles interact with each other, forming new blood vessels either from the existing ones or from a primary vascular plexus, is particularly important and interesting, due to new therapeutic possibilities it offers. This is a multi-step and very complex process, so an accurate understanding of the underlying mechanisms is a significant task, especially in recent years, with the constantly increasing amount of new data that must be taken into account. A systems approach is necessary for these studies because it is not sufficient to analyze the properties of the building blocks separately and an analysis of the whole network of interactions is essential. This approach is based on building a mathematical model of the system, while the model is expressed in the formal language of a mathematical theory. Recently, the theory of Petri nets was shown to be especially promising for the modeling and analysis of biological phenomena. This analysis, based mainly on t-invariants, has led to a particularly important finding that a direct link (close connection) exist between transforming growth factor β1 (TGF-β1), endothelial nitric oxide synthase (eNOS), nitric oxide (NO), and hypoxia-inducible factor 1, the molecules that play a crucial roles during angiogenesis. We have shown that TGF-β1 may participate in the inhibition of angiogenesis through the upregulation of eNOS expression, which is responsible for catalyzing NO production. The results obtained in the previous studies, concerning the effects of NO on angiogenesis, have not been conclusive, and therefore, our study may contribute to a better understanding of this phenomenon. PMID:28253310

Petri net-based approach to modeling and analysis of selected aspects of the molecular regulation of angiogenesis.

PubMed

Formanowicz, Dorota; Radom, Marcin; Zawierucha, Piotr; Formanowicz, Piotr

2017-01-01

The functioning of both normal and pathological tissues depends on an adequate supply of oxygen through the blood vessels. A process called angiogenesis, in which new endothelial cells and smooth muscles interact with each other, forming new blood vessels either from the existing ones or from a primary vascular plexus, is particularly important and interesting, due to new therapeutic possibilities it offers. This is a multi-step and very complex process, so an accurate understanding of the underlying mechanisms is a significant task, especially in recent years, with the constantly increasing amount of new data that must be taken into account. A systems approach is necessary for these studies because it is not sufficient to analyze the properties of the building blocks separately and an analysis of the whole network of interactions is essential. This approach is based on building a mathematical model of the system, while the model is expressed in the formal language of a mathematical theory. Recently, the theory of Petri nets was shown to be especially promising for the modeling and analysis of biological phenomena. This analysis, based mainly on t-invariants, has led to a particularly important finding that a direct link (close connection) exist between transforming growth factor β1 (TGF-β1), endothelial nitric oxide synthase (eNOS), nitric oxide (NO), and hypoxia-inducible factor 1, the molecules that play a crucial roles during angiogenesis. We have shown that TGF-β1 may participate in the inhibition of angiogenesis through the upregulation of eNOS expression, which is responsible for catalyzing NO production. The results obtained in the previous studies, concerning the effects of NO on angiogenesis, have not been conclusive, and therefore, our study may contribute to a better understanding of this phenomenon.

Construction and Experimental Validation of a Petri Net Model of Wnt/β-Catenin Signaling

PubMed Central

Heijmans, Nika; Verkaar, Folkert; Smit, Martine J.; Heringa, Jaap

2016-01-01

The Wnt/β-catenin signaling pathway is important for multiple developmental processes and tissue maintenance in adults. Consequently, deregulated signaling is involved in a range of human diseases including cancer and developmental defects. A better understanding of the intricate regulatory mechanism and effect of physiological (active) and pathophysiological (hyperactive) WNT signaling is important for predicting treatment response and developing novel therapies. The constitutively expressed CTNNB1 (commonly and hereafter referred to as β-catenin) is degraded by a destruction complex, composed of amongst others AXIN1 and GSK3. The destruction complex is inhibited during active WNT signaling, leading to β-catenin stabilization and induction of β-catenin/TCF target genes. In this study we investigated the mechanism and effect of β-catenin stabilization during active and hyperactive WNT signaling in a combined in silico and in vitro approach. We constructed a Petri net model of Wnt/β-catenin signaling including main players from the plasma membrane (WNT ligands and receptors), cytoplasmic effectors and the downstream negative feedback target gene AXIN2. We validated that our model can be used to simulate both active (WNT stimulation) and hyperactive (GSK3 inhibition) signaling by comparing our simulation and experimental data. We used this experimentally validated model to get further insights into the effect of the negative feedback regulator AXIN2 upon WNT stimulation and observed an attenuated β-catenin stabilization. We furthermore simulated the effect of APC inactivating mutations, yielding a stabilization of β-catenin levels comparable to the Wnt-pathway activities observed in colorectal and breast cancer. Our model can be used for further investigation and viable predictions of the role of Wnt/β-catenin signaling in oncogenesis and development. PMID:27218469

Petri-Net Simulations of Communications Networks.

DTIC Science & Technology

1980-03-01

place, althcugh in reality they may be buried several deep. As the total network is conceptualized by the user. he irust betin by mappinp out all oripins...8217 . (choCk~mahes(z*11)!1𔃺’) 957 ockt2(x,y,’nark-,colour);’I 95 elsef 960 if((check~namesrz.Il 1:’) rt(xl405.(v2i"mr) 134 traflloraph.c PaQ * 17 Fri Feb 8...Iaxnctrk+*) l0g0 intbl1.; 164 lirnkgrach.c paq * 19 Fri Feb 8 07:0q:45 1980 1081 in (k[) miot I Iintbi I; 10(42 1 1083 iawoutctr:iolr,1(outtb1l; 1084

Modeling of dialogue regimes of distance robot control

NASA Astrophysics Data System (ADS)

Larkin, E. V.; Privalov, A. N.

2017-02-01

Process of distance control of mobile robots is investigated. Petri-Markov net for modeling of dialogue regime is worked out. It is shown, that sequence of operations of next subjects: a human operator, a dialogue computer and an onboard computer may be simulated with use the theory of semi-Markov processes. From the semi-Markov process of the general form Markov process was obtained, which includes only states of transaction generation. It is shown, that a real transaction flow is the result of «concurrency» in states of Markov process. Iteration procedure for evaluation of transaction flow parameters, which takes into account effect of «concurrency», is proposed.

A neural network simulation package in CLIPS

NASA Technical Reports Server (NTRS)

Bhatnagar, Himanshu; Krolak, Patrick D.; Mcgee, Brenda J.; Coleman, John

1990-01-01

The intrinsic similarity between the firing of a rule and the firing of a neuron has been captured in this research to provide a neural network development system within an existing production system (CLIPS). A very important by-product of this research has been the emergence of an integrated technique of using rule based systems in conjunction with the neural networks to solve complex problems. The systems provides a tool kit for an integrated use of the two techniques and is also extendible to accommodate other AI techniques like the semantic networks, connectionist networks, and even the petri nets. This integrated technique can be very useful in solving complex AI problems.

AFRRI (Armed Forces Radiobiology Research Institute) Reports, July, August and September 1987.

DTIC Science & Technology

1987-11-01

mononuclear cell layer obtained after Percol isolation contained approximately 90% mono- cytes as assessed by esterase staining. In most experiments...forming cell) were assayed using the double layer agar technique basically as described by Hagan et al. (22). The culture medium was double strength CMRL...trypticase soy broth, 20 g/ml L-asparagine. and penicillin-streptomycin. In the bottom layer of 35 mm plastic Petri dishes was 1 ml of a 1:1 mixture of culture

DOE Office of Scientific and Technical Information (OSTI.GOV)

Mather, James

Atmospheric Radiation Measurement (ARM) Program standard data format is NetCDF 3 (Network Common Data Form). The object of this tutorial is to provide a basic introduction to NetCDF with an emphasis on aspects of the ARM application of NetCDF. The goal is to provide basic instructions for reading and visualizing ARM NetCDF data with the expectation that these examples can then be applied to more complex applications.

CyberPetri at CDX 2016: Real-time Network Situation Awareness

DOE Office of Scientific and Technical Information (OSTI.GOV)

Arendt, Dustin L.; Best, Daniel M.; Burtner, Edwin R.

CyberPetri is a novel visualization technique that provides a flexible map of the network based on available characteristics, such as IP address, operating system, or service. Previous work introduced CyberPetri as a visualization feature in Ocelot, a network defense tool that helped security analysts understand and respond to an active defense scenario. In this paper we present a case study in which we use the CyberPetri visualization technique to support real-time situation awareness during the 2016 Cyber Defense Exercise.

Client - server programs analysis in the EPOCA environment

NASA Astrophysics Data System (ADS)

Donatelli, Susanna; Mazzocca, Nicola; Russo, Stefano

1996-09-01

Client - server processing is a popular paradigm for distributed computing. In the development of client - server programs, the designer has first to ensure that the implementation behaves correctly, in particular that it is deadlock free. Second, he has to guarantee that the program meets predefined performance requirements. This paper addresses the issues in the analysis of client - server programs in EPOCA. EPOCA is a computer-aided software engeneering (CASE) support system that allows the automated construction and analysis of generalized stochastic Petri net (GSPN) models of concurrent applications. The paper describes, on the basis of a realistic case study, how client - server systems are modelled in EPOCA, and the kind of qualitative and quantitative analysis supported by its tools.

Telerobotic management system: coordinating multiple human operators with multiple robots

NASA Astrophysics Data System (ADS)

King, Jamie W.; Pretty, Raymond; Brothers, Brendan; Gosine, Raymond G.

2003-09-01

This paper describes an application called the Tele-robotic management system (TMS) for coordinating multiple operators with multiple robots for applications such as underground mining. TMS utilizes several graphical interfaces to allow the user to define a partially ordered plan for multiple robots. This plan is then converted to a Petri net for execution and monitoring. TMS uses a distributed framework to allow robots and operators to easily integrate with the applications. This framework allows robots and operators to join the network and advertise their capabilities through services. TMS then decides whether tasks should be dispatched to a robot or a remote operator based on the services offered by the robots and operators.

DEVELOPMENT OF USER-FRIENDLY SIMULATION SYSTEM OF EARTHQUAKE INDUCED URBAN SPREADING FIRE

NASA Astrophysics Data System (ADS)

Tsujihara, Osamu; Gawa, Hidemi; Hayashi, Hirofumi

In the simulation of earthquake induced urban spreading fire, the produce of the analytical model of the target area is required as well as the analysis of spreading fire and the presentati on of the results. In order to promote the use of the simulation, it is important that the simulation system is non-intrusive and the analysis results can be demonstrated by the realistic presentation. In this study, the simulation system is developed based on the Petri-net algorithm, in which the easy operation can be realized in the modeling of the target area of the simulation through the presentation of analytical results by realistic 3-D animation.

Hierarchical Coloured Petrinet Based Healthcare Infrastructure Interdependency Model

NASA Astrophysics Data System (ADS)

Nivedita, N.; Durbha, S.

2014-11-01

To ensure a resilient Healthcare Critical Infrastructure, understanding the vulnerabilities and analysing the interdependency on other critical infrastructures is important. To model this critical infrastructure and its dependencies, Hierarchal Coloured petri net modelling approach for simulating the vulnerability of Healthcare Critical infrastructure in a disaster situation is studied.. The model enables to analyse and understand various state changes, which occur when there is a disruption or damage to any of the Critical Infrastructure, and its cascading nature. It also enables to explore optimal paths for evacuation during the disaster. The simulation environment can be used to understand and highlight various vulnerabilities of Healthcare Critical Infrastructure during a flood disaster scenario; minimize consequences; and enable timely, efficient response.

Safety Discrete Event Models for Holonic Cyclic Manufacturing Systems

NASA Astrophysics Data System (ADS)

Ciufudean, Calin; Filote, Constantin

In this paper the expression “holonic cyclic manufacturing systems” refers to complex assembly/disassembly systems or fork/join systems, kanban systems, and in general, to any discrete event system that transforms raw material and/or components into products. Such a system is said to be cyclic if it provides the same sequence of products indefinitely. This paper considers the scheduling of holonic cyclic manufacturing systems and describes a new approach using Petri nets formalism. We propose an approach to frame the optimum schedule of holonic cyclic manufacturing systems in order to maximize the throughput while minimize the work in process. We also propose an algorithm to verify the optimum schedule.

Validation of a SysML based design for wireless sensor networks

NASA Astrophysics Data System (ADS)

Berrachedi, Amel; Rahim, Messaoud; Ioualalen, Malika; Hammad, Ahmed

2017-07-01

When developing complex systems, the requirement for the verification of the systems' design is one of the main challenges. Wireless Sensor Networks (WSNs) are examples of such systems. We address the problem of how WSNs must be designed to fulfil the system requirements. Using the SysML Language, we propose a Model Based System Engineering (MBSE) specification and verification methodology for designing WSNs. This methodology uses SysML to describe the WSNs requirements, structure and behaviour. Then, it translates the SysML elements to an analytic model, specifically, to a Deterministic Stochastic Petri Net. The proposed approach allows to design WSNs and study their behaviors and their energy performances.

The Net Neutrality Debate: The Basics

ERIC Educational Resources Information Center

Greenfield, Rich

2006-01-01

Rich Greenfield examines the basics of today's net neutrality debate that is likely to be an ongoing issue for society. Greenfield states the problems inherent in the definition of "net neutrality" used by Common Cause: "Network neutrality is the principle that Internet users should be able to access any web content they choose and…

SHER: a colored petri net based random mobility model for wireless communications.

PubMed

Khan, Naeem Akhtar; Ahmad, Farooq; Khan, Sher Afzal

2015-01-01

In wireless network research, simulation is the most imperative technique to investigate the network's behavior and validation. Wireless networks typically consist of mobile hosts; therefore, the degree of validation is influenced by the underlying mobility model, and synthetic models are implemented in simulators because real life traces are not widely available. In wireless communications, mobility is an integral part while the key role of a mobility model is to mimic the real life traveling patterns to study. The performance of routing protocols and mobility management strategies e.g. paging, registration and handoff is highly dependent to the selected mobility model. In this paper, we devise and evaluate the Show Home and Exclusive Regions (SHER), a novel two-dimensional (2-D) Colored Petri net (CPN) based formal random mobility model, which exhibits sociological behavior of a user. The model captures hotspots where a user frequently visits and spends time. Our solution eliminates six key issues of the random mobility models, i.e., sudden stops, memoryless movements, border effect, temporal dependency of velocity, pause time dependency, and speed decay in a single model. The proposed model is able to predict the future location of a mobile user and ultimately improves the performance of wireless communication networks. The model follows a uniform nodal distribution and is a mini simulator, which exhibits interesting mobility patterns. The model is also helpful to those who are not familiar with the formal modeling, and users can extract meaningful information with a single mouse-click. It is noteworthy that capturing dynamic mobility patterns through CPN is the most challenging and virulent activity of the presented research. Statistical and reachability analysis techniques are presented to elucidate and validate the performance of our proposed mobility model. The state space methods allow us to algorithmically derive the system behavior and rectify the errors of our proposed model.

SHER: A Colored Petri Net Based Random Mobility Model for Wireless Communications

PubMed Central

Khan, Naeem Akhtar; Ahmad, Farooq; Khan, Sher Afzal

2015-01-01

In wireless network research, simulation is the most imperative technique to investigate the network’s behavior and validation. Wireless networks typically consist of mobile hosts; therefore, the degree of validation is influenced by the underlying mobility model, and synthetic models are implemented in simulators because real life traces are not widely available. In wireless communications, mobility is an integral part while the key role of a mobility model is to mimic the real life traveling patterns to study. The performance of routing protocols and mobility management strategies e.g. paging, registration and handoff is highly dependent to the selected mobility model. In this paper, we devise and evaluate the Show Home and Exclusive Regions (SHER), a novel two-dimensional (2-D) Colored Petri net (CPN) based formal random mobility model, which exhibits sociological behavior of a user. The model captures hotspots where a user frequently visits and spends time. Our solution eliminates six key issues of the random mobility models, i.e., sudden stops, memoryless movements, border effect, temporal dependency of velocity, pause time dependency, and speed decay in a single model. The proposed model is able to predict the future location of a mobile user and ultimately improves the performance of wireless communication networks. The model follows a uniform nodal distribution and is a mini simulator, which exhibits interesting mobility patterns. The model is also helpful to those who are not familiar with the formal modeling, and users can extract meaningful information with a single mouse-click. It is noteworthy that capturing dynamic mobility patterns through CPN is the most challenging and virulent activity of the presented research. Statistical and reachability analysis techniques are presented to elucidate and validate the performance of our proposed mobility model. The state space methods allow us to algorithmically derive the system behavior and rectify the errors of our proposed model. PMID:26267860

An integrated pathway system modeling of Saccharomyces cerevisiae HOG pathway: a Petri net based approach.

PubMed

Tomar, Namrata; Choudhury, Olivia; Chakrabarty, Ankush; De, Rajat K

2013-02-01

Biochemical networks comprise many diverse components and interactions between them. It has intracellular signaling, metabolic and gene regulatory pathways which are highly integrated and whose responses are elicited by extracellular actions. Previous modeling techniques mostly consider each pathway independently without focusing on the interrelation of these which actually functions as a single system. In this paper, we propose an approach of modeling an integrated pathway using an event-driven modeling tool, i.e., Petri nets (PNs). PNs have the ability to simulate the dynamics of the system with high levels of accuracy. The integrated set of signaling, regulatory and metabolic reactions involved in Saccharomyces cerevisiae's HOG pathway has been collected from the literature. The kinetic parameter values have been used for transition firings. The dynamics of the system has been simulated and the concentrations of major biological species over time have been observed. The phenotypic characteristics of the integrated system have been investigated under two conditions, viz., under the absence and presence of osmotic pressure. The results have been validated favorably with the existing experimental results. We have also compared our study with the study of idFBA (Lee et al., PLoS Comput Biol 4:e1000-e1086, 2008) and pointed out the differences between both studies. We have simulated and monitored concentrations of multiple biological entities over time and also incorporated feedback inhibition by Ptp2 which has not been included in the idFBA study. We have concluded that our study is the first to the best of our knowledge to model signaling, metabolic and regulatory events in an integrated form through PN model framework. This study is useful in computational simulation of system dynamics for integrated pathways as there are growing evidences that the malfunctioning of the interplay among these pathways is associated with disease.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2011-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier. Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

Exhaustive analysis of the modular structure of the spliceosomal assembly network: a Petri net approach.

PubMed

Bortfeldt, Ralf H; Schuster, Stefan; Koch, Ina

2010-01-01

Spliceosomes are macro-complexes involving hundreds of proteins with many functional interactions. Spliceosome assembly belongs to the key processes that enable splicing of mRNA and modulate alternative splicing. A detailed list of factors involved in spliceosomal reactions has been assorted over the past decade, but, their functional interplay is often unknown and most of the present biological models cover only parts of the complete assembly process. It is a challenging task to build a computational model that integrates dispersed knowledge and combines a multitude of reaction schemes proposed earlier.Because for most reactions involved in spliceosome assembly kinetic parameters are not available, we propose a discrete modeling using Petri nets, through which we are enabled to get insights into the system's behavior via computation of structural and dynamic properties. In this paper, we compile and examine reactions from experimental reports that contribute to a functional spliceosome. All these reactions form a network, which describes the inventory and conditions necessary to perform the splicing process. The analysis is mainly based on system invariants. Transition invariants (T-invariants) can be interpreted as signaling routes through the network. Due to the huge number of T-invariants that arise with increasing network size and complexity, maximal common transition sets (MCTS) and T-clusters were used for further analysis. Additionally, we introduce a false color map representation, which allows a quick survey of network modules and the visual detection of single reactions or reaction sequences, which participate in more than one signaling route. We designed a structured model of spliceosome assembly, which combines the demands on a platform that i) can display involved factors and concurrent processes, ii) offers the possibility to run computational methods for knowledge extraction, and iii) is successively extendable as new insights into spliceosome function are reported by experimental reports. The network consists of 161 transitions (reactions) and 140 places (reactants). All reactions are part of at least one of the 71 T-invariants. These T-invariants define pathways, which are in good agreement with the current knowledge and known hypotheses on reaction sequences during spliceosome assembly, hence contributing to a functional spliceosome. We demonstrate that present knowledge, in particular of the initial part of the assembly process, describes parallelism and interaction of signaling routes, which indicate functional redundancy and reflect the dependency of spliceosome assembly initiation on different cellular conditions. The complexity of the network is further increased by two switches, which introduce alternative routes during A-complex formation in early spliceosome assembly and upon transition from the B-complex to the C-complex. By compiling known reactions into a complete network, the combinatorial nature of invariant computation leads to pathways that have previously not been described as connected routes, although their constituents were known. T-clusters divide the network into modules, which we interpret as building blocks in spliceosome maturation. We conclude that Petri net representations of large biological networks and system invariants, are well-suited as a means for validating the integration of experimental knowledge into a consistent model. Based on this network model, the design of further experiments is facilitated.

A computer architecture for intelligent machines

NASA Technical Reports Server (NTRS)

Lefebvre, D. R.; Saridis, G. N.

1992-01-01

The theory of intelligent machines proposes a hierarchical organization for the functions of an autonomous robot based on the principle of increasing precision with decreasing intelligence. An analytic formulation of this theory using information-theoretic measures of uncertainty for each level of the intelligent machine has been developed. The authors present a computer architecture that implements the lower two levels of the intelligent machine. The architecture supports an event-driven programming paradigm that is independent of the underlying computer architecture and operating system. Execution-level controllers for motion and vision systems are briefly addressed, as well as the Petri net transducer software used to implement coordination-level functions. A case study illustrates how this computer architecture integrates real-time and higher-level control of manipulator and vision systems.

Modelling and temporal performances evaluation of networked control systems using (max, +) algebra

NASA Astrophysics Data System (ADS)

Ammour, R.; Amari, S.

2015-01-01

In this paper, we address the problem of temporal performances evaluation of producer/consumer networked control systems. The aim is to develop a formal method for evaluating the response time of this type of control systems. Our approach consists on modelling, using Petri nets classes, the behaviour of the whole architecture including the switches that support multicast communications used by this protocol. (max, +) algebra formalism is then exploited to obtain analytical formulas of the response time and the maximal and minimal bounds. The main novelty is that our approach takes into account all delays experienced at the different stages of networked automation systems. Finally, we show how to apply the obtained results through an example of networked control system.

Fault-tolerant continuous flow systems modelling

NASA Astrophysics Data System (ADS)

Tolbi, B.; Tebbikh, H.; Alla, H.

2017-01-01

This paper presents a structural modelling of faults with hybrid Petri nets (HPNs) for the analysis of a particular class of hybrid dynamic systems, continuous flow systems. HPNs are first used for the behavioural description of continuous flow systems without faults. Then, faults' modelling is considered using a structural method without having to rebuild the model to new. A translation method is given in hierarchical way, it gives a hybrid automata (HA) from an elementary HPN. This translation preserves the behavioural semantics (timed bisimilarity), and reflects the temporal behaviour by giving semantics for each model in terms of timed transition systems. Thus, advantages of the power modelling of HPNs and the analysis ability of HA are taken. A simple example is used to illustrate the ideas.

Case study: Optimizing fault model input parameters using bio-inspired algorithms

NASA Astrophysics Data System (ADS)

Plucar, Jan; Grunt, Onřej; Zelinka, Ivan

2017-07-01

We present a case study that demonstrates a bio-inspired approach in the process of finding optimal parameters for GSM fault model. This model is constructed using Petri Nets approach it represents dynamic model of GSM network environment in the suburban areas of Ostrava city (Czech Republic). We have been faced with a task of finding optimal parameters for an application that requires high amount of data transfers between the application itself and secure servers located in datacenter. In order to find the optimal set of parameters we employ bio-inspired algorithms such as Differential Evolution (DE) or Self Organizing Migrating Algorithm (SOMA). In this paper we present use of these algorithms, compare results and judge their performance in fault probability mitigation.

Qualitative modeling of normal blood coagulation and its pathological states using stochastic activity networks.

PubMed

Mounts, W M; Liebman, M N

1997-07-01

We have developed a method for representing biological pathways and simulating their behavior based on the use of stochastic activity networks (SANs). SANs, an extension of the original Petri net, have been used traditionally to model flow systems including data-communications networks and manufacturing processes. We apply the methodology to the blood coagulation cascade, a biological flow system, and present the representation method as well as results of simulation studies based on published experimental data. In addition to describing the dynamic model, we also present the results of its utilization to perform simulations of clinical states including hemophilia's A and B as well as sensitivity analysis of individual factors and their impact on thrombin production.

Testing of Compounds for Efficacy against Schistosomiasis.

DTIC Science & Technology

1986-07-22

4); 2) a petri dish containing a centrally placed mud mound, blue-green aglae ( Nostoc muscorum) and water Is used for rearing young snails and...maintaining both pre-exposed and exposed snails (5); 3) a petri dish containing small amounts of blue-green algae ( Nostoc muscoru), mud and water is used...25-27 C. 4. Food. Blue-green algae ( Nostoc muscorum) grown in petri dishes with mud (5) is used exclusively as the food source. C. Breedin A

Photocatalytic bacterial inactivation by TiO2-coated surfaces

PubMed Central

2013-01-01

The aim of this study was the evaluation of the photoactivated antibacterial activity of titanium dioxide (TiO2)-coated surfaces. Bacterial inactivation was evaluated using TiO2-coated Petri dishes. The experimental conditions optimized with Petri dishes were used to test the antibacterial effect of TiO2-coated ceramic tiles. The best antibacterial effect with Petri dishes was observed at 180, 60, 30 and 20 min of exposure for Escherichia coli, Staphylococcus aureus, Pseudomonas putida and Listeria innocua, respectively. The ceramic tiles demonstrated a photoactivated bactericidal effect at the same exposure time. In general, no differences were observed between the antibacterial effect obtained with Petri dishes and tiles. However, the photochemical activity of Petri dishes was greater than the activity of the tiles. Results obtained indicates that the TiO2-coated surfaces showed a photoactivated bactericidal effect with all bacteria tested highlighting that the titania could be used in the ceramic and building industry for the production of coated surfaces to be placed in microbiologically sensitive environments, such as the hospital and food industry. PMID:24090112

Modeling formalisms in Systems Biology

PubMed Central

2011-01-01

Systems Biology has taken advantage of computational tools and high-throughput experimental data to model several biological processes. These include signaling, gene regulatory, and metabolic networks. However, most of these models are specific to each kind of network. Their interconnection demands a whole-cell modeling framework for a complete understanding of cellular systems. We describe the features required by an integrated framework for modeling, analyzing and simulating biological processes, and review several modeling formalisms that have been used in Systems Biology including Boolean networks, Bayesian networks, Petri nets, process algebras, constraint-based models, differential equations, rule-based models, interacting state machines, cellular automata, and agent-based models. We compare the features provided by different formalisms, and discuss recent approaches in the integration of these formalisms, as well as possible directions for the future. PMID:22141422

Intelligent Operation and Maintenance of Micro-grid Technology and System Development

NASA Astrophysics Data System (ADS)

Fu, Ming; Song, Jinyan; Zhao, Jingtao; Du, Jian

2018-01-01

In order to achieve the micro-grid operation and management, Studying the micro-grid operation and maintenance knowledge base. Based on the advanced Petri net theory, the fault diagnosis model of micro-grid is established, and the intelligent diagnosis and analysis method of micro-grid fault is put forward. Based on the technology, the functional system and architecture of the intelligent operation and maintenance system of micro-grid are studied, and the microcomputer fault diagnosis function is introduced in detail. Finally, the system is deployed based on the micro-grid of a park, and the micro-grid fault diagnosis and analysis is carried out based on the micro-grid operation. The system operation and maintenance function interface is displayed, which verifies the correctness and reliability of the system.

Simulator for heterogeneous dataflow architectures

NASA Technical Reports Server (NTRS)

Malekpour, Mahyar R.

1993-01-01

A new simulator is developed to simulate the execution of an algorithm graph in accordance with the Algorithm to Architecture Mapping Model (ATAMM) rules. ATAMM is a Petri Net model which describes the periodic execution of large-grained, data-independent dataflow graphs and which provides predictable steady state time-optimized performance. This simulator extends the ATAMM simulation capability from a heterogenous set of resources, or functional units, to a more general heterogenous architecture. Simulation test cases show that the simulator accurately executes the ATAMM rules for both a heterogenous architecture and a homogenous architecture, which is the special case for only one processor type. The simulator forms one tool in an ATAMM Integrated Environment which contains other tools for graph entry, graph modification for performance optimization, and playback of simulations for analysis.

Optimization of airport security process

NASA Astrophysics Data System (ADS)

Wei, Jianan

2017-05-01

In order to facilitate passenger travel, on the basis of ensuring public safety, the airport security process and scheduling to optimize. The stochastic Petri net is used to simulate the single channel security process, draw the reachable graph, construct the homogeneous Markov chain to realize the performance analysis of the security process network, and find the bottleneck to limit the passenger throughput. Curve changes in the flow of passengers to open a security channel for the initial state. When the passenger arrives at a rate that exceeds the processing capacity of the security channel, it is queued. The passenger reaches the acceptable threshold of the queuing time as the time to open or close the next channel, simulate the number of dynamic security channel scheduling to reduce the passenger queuing time.

Automated synthesis and composition of taskblocks for control of manufacturing systems.

PubMed

Holloway, L E; Guan, X; Sundaravadivelu, R; Ashley, J R

2000-01-01

Automated control synthesis methods for discrete-event systems promise to reduce the time required to develop, debug, and modify control software. Such methods must be able to translate high-level control goals into detailed sequences of actuation and sensing signals. In this paper, we present such a technique. It relies on analysis of a system model, defined as a set of interacting components, each represented as a form of condition system Petri net. Control logic modules, called taskblocks, are synthesized from these individual models. These then interact hierarchically and sequentially to drive the system through specified control goals. The resulting controller is automatically converted to executable control code. The paper concludes with a discussion of a set of software tools developed to demonstrate the techniques on a small manufacturing system.

Wakata performs microscopic analysis of the NanoRacks Module-38 Petri Dishes

NASA Image and Video Library

2014-01-13

ISS038-E-029082 (12 Jan. 2014) --- Japan Aerospace Exploration Agency astronaut Koichi Wakata, Expedition 38 flight engineer, performs microscopic analysis of the NanoRacks Module-38 Petri Dishes, using Celestron Reflective Microscope, in the Kibo laboratory of the International Space Station. These Module-38 experiments are designed by students as part of a competition sponsored by the International Space School Educational Trust (ISSET). This experiment examines three-dimensional growth of slime mold in petri dishes utilizing the NanoRacks Microscopes Facility.

PhysioNet: physiologic signals, time series and related open source software for basic, clinical, and applied research.

PubMed

Moody, George B; Mark, Roger G; Goldberger, Ary L

2011-01-01

PhysioNet provides free web access to over 50 collections of recorded physiologic signals and time series, and related open-source software, in support of basic, clinical, and applied research in medicine, physiology, public health, biomedical engineering and computing, and medical instrument design and evaluation. Its three components (PhysioBank, the archive of signals; PhysioToolkit, the software library; and PhysioNetWorks, the virtual laboratory for collaborative development of future PhysioBank data collections and PhysioToolkit software components) connect researchers and students who need physiologic signals and relevant software with researchers who have data and software to share. PhysioNet's annual open engineering challenges stimulate rapid progress on unsolved or poorly solved questions of basic or clinical interest, by focusing attention on achievable solutions that can be evaluated and compared objectively using freely available reference data.

Test Bank. NetNews. Volume 8, Number 1, Winter 2008

ERIC Educational Resources Information Center

LDA of Minnesota, 2008

2008-01-01

Minnesota Adult Basic Education (ABE) providers are mandated to use CASAS (Comprehensive Adult Student Assessment System) Reading or Math or TABE (Tests for Adult Basic Education) Reading or Math. This issue of "NetNews" introduces the Test Bank: a variety of informal reading, spelling, and writing assessments available for Minnesota ABE…

Creating executable architectures using Visual Simulation Objects (VSO)

NASA Astrophysics Data System (ADS)

Woodring, John W.; Comiskey, John B.; Petrov, Orlin M.; Woodring, Brian L.

2005-05-01

Investigations have been performed to identify a methodology for creating executable models of architectures and simulations of architecture that lead to an understanding of their dynamic properties. Colored Petri Nets (CPNs) are used to describe architecture because of their strong mathematical foundations, the existence of techniques for their verification and graph theory"s well-established history of success in modern science. CPNs have been extended to interoperate with legacy simulations via a High Level Architecture (HLA) compliant interface. It has also been demonstrated that an architecture created as a CPN can be integrated with Department of Defense Architecture Framework products to ensure consistency between static and dynamic descriptions. A computer-aided tool, Visual Simulation Objects (VSO), which aids analysts in specifying, composing and executing architectures, has been developed to verify the methodology and as a prototype commercial product.

Simple methods of exploiting the underlying structure of rule-based systems

NASA Technical Reports Server (NTRS)

Hendler, James

1986-01-01

Much recent work in the field of expert systems research has aimed at exploiting the underlying structures of the rule base for reasons of analysis. Such techniques as Petri-nets and GAGs have been proposed as representational structures that will allow complete analysis. Much has been made of proving isomorphisms between the rule bases and the mechanisms, and in examining the theoretical power of this analysis. In this paper we describe some early work in a new system which has much simpler (and thus, one hopes, more easily achieved) aims and less formality. The technique being examined is a very simple one: OPS5 programs are analyzed in a purely syntactic way and a FSA description is generated. In this paper we describe the technique and some user interface tools which exploit this structure.

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon W.; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are normally delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

A patient workflow management system built on guidelines.

PubMed Central

Dazzi, L.; Fassino, C.; Saracco, R.; Quaglini, S.; Stefanelli, M.

1997-01-01

To provide high quality, shared, and distributed medical care, clinical and organizational issues need to be integrated. This work describes a methodology for developing a Patient Workflow Management System, based on a detailed model of both the medical work process and the organizational structure. We assume that the medical work process is represented through clinical practice guidelines, and that an ontological description of the organization is available. Thus, we developed tools 1) for acquiring the medical knowledge contained into a guideline, 2) to translate the derived formalized guideline into a computational formalism, precisely a Petri Net, 3) to maintain different representation levels. The high level representation guarantees that the Patient Workflow follows the guideline prescriptions, while the low level takes into account the specific organization characteristics and allow allocating resources for managing a specific patient in daily practice. PMID:9357606

Simulation in a dynamic prototyping environment: Petri nets or rules?

NASA Technical Reports Server (NTRS)

Moore, Loretta A.; Price, Shannon; Hale, Joseph P.

1994-01-01

An evaluation of a prototyped user interface is best supported by a simulation of the system. A simulation allows for dynamic evaluation of the interface rather than just a static evaluation of the screen's appearance. This allows potential users to evaluate both the look (in terms of the screen layout, color, objects, etc.) and feel (in terms of operations and actions which need to be performed) of a system's interface. Because of the need to provide dynamic evaluation of an interface, there must be support for producing active simulations. The high-fidelity training simulators are delivered too late to be effectively used in prototyping the displays. Therefore, it is important to build a low fidelity simulator, so that the iterative cycle of refining the human computer interface based upon a user's interactions can proceed early in software development.

Deadlock-free genetic scheduling algorithm for automated manufacturing systems based on deadlock control policy.

PubMed

Xing, KeYi; Han, LiBin; Zhou, MengChu; Wang, Feng

2012-06-01

Deadlock-free control and scheduling are vital for optimizing the performance of automated manufacturing systems (AMSs) with shared resources and route flexibility. Based on the Petri net models of AMSs, this paper embeds the optimal deadlock avoidance policy into the genetic algorithm and develops a novel deadlock-free genetic scheduling algorithm for AMSs. A possible solution of the scheduling problem is coded as a chromosome representation that is a permutation with repetition of parts. By using the one-step look-ahead method in the optimal deadlock control policy, the feasibility of a chromosome is checked, and infeasible chromosomes are amended into feasible ones, which can be easily decoded into a feasible deadlock-free schedule. The chromosome representation and polynomial complexity of checking and amending procedures together support the cooperative aspect of genetic search for scheduling problems strongly.

Formal specification and design techniques for wireless sensor and actuator networks.

PubMed

Martínez, Diego; González, Apolinar; Blanes, Francisco; Aquino, Raúl; Simo, José; Crespo, Alfons

2011-01-01

A current trend in the development and implementation of industrial applications is to use wireless networks to communicate the system nodes, mainly to increase application flexibility, reliability and portability, as well as to reduce the implementation cost. However, the nondeterministic and concurrent behavior of distributed systems makes their analysis and design complex, often resulting in less than satisfactory performance in simulation and test bed scenarios, which is caused by using imprecise models to analyze, validate and design these systems. Moreover, there are some simulation platforms that do not support these models. This paper presents a design and validation method for Wireless Sensor and Actuator Networks (WSAN) which is supported on a minimal set of wireless components represented in Colored Petri Nets (CPN). In summary, the model presented allows users to verify the design properties and structural behavior of the system.

United States Navy Oceanic Armed Reconnaissance System

DTIC Science & Technology

2011-12-12

This report was prepared by: Rahul Petrie Daniel Reese Kurtis Hoots Robert Taylor Drew Nash Bunny Cooper Jonathan Trdan-Schmidt Marshall...NPS – Cohort 311-102S, Team OARS: Mr. Marshall Rice, Mr. Rahul Petrie, Mr. Daniel Reese, Mr. Kurtis Hoots, Mr. Robert Taylor, Mr. Drew Nash

Formal Specification and Design Techniques for Wireless Sensor and Actuator Networks

PubMed Central

Martínez, Diego; González, Apolinar; Blanes, Francisco; Aquino, Raúl; Simo, José; Crespo, Alfons

2011-01-01

A current trend in the development and implementation of industrial applications is to use wireless networks to communicate the system nodes, mainly to increase application flexibility, reliability and portability, as well as to reduce the implementation cost. However, the nondeterministic and concurrent behavior of distributed systems makes their analysis and design complex, often resulting in less than satisfactory performance in simulation and test bed scenarios, which is caused by using imprecise models to analyze, validate and design these systems. Moreover, there are some simulation platforms that do not support these models. This paper presents a design and validation method for Wireless Sensor and Actuator Networks (WSAN) which is supported on a minimal set of wireless components represented in Colored Petri Nets (CPN). In summary, the model presented allows users to verify the design properties and structural behavior of the system. PMID:22344203

Data flow modeling techniques

NASA Technical Reports Server (NTRS)

Kavi, K. M.

1984-01-01

There have been a number of simulation packages developed for the purpose of designing, testing and validating computer systems, digital systems and software systems. Complex analytical tools based on Markov and semi-Markov processes have been designed to estimate the reliability and performance of simulated systems. Petri nets have received wide acceptance for modeling complex and highly parallel computers. In this research data flow models for computer systems are investigated. Data flow models can be used to simulate both software and hardware in a uniform manner. Data flow simulation techniques provide the computer systems designer with a CAD environment which enables highly parallel complex systems to be defined, evaluated at all levels and finally implemented in either hardware or software. Inherent in data flow concept is the hierarchical handling of complex systems. In this paper we will describe how data flow can be used to model computer system.

Comprehensive Quantitative Analysis on Privacy Leak Behavior

PubMed Central

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects. PMID:24066046

Comprehensive quantitative analysis on privacy leak behavior.

PubMed

Fan, Lejun; Wang, Yuanzhuo; Jin, Xiaolong; Li, Jingyuan; Cheng, Xueqi; Jin, Shuyuan

2013-01-01

Privacy information is prone to be leaked by illegal software providers with various motivations. Privacy leak behavior has thus become an important research issue of cyber security. However, existing approaches can only qualitatively analyze privacy leak behavior of software applications. No quantitative approach, to the best of our knowledge, has been developed in the open literature. To fill this gap, in this paper we propose for the first time four quantitative metrics, namely, possibility, severity, crypticity, and manipulability, for privacy leak behavior analysis based on Privacy Petri Net (PPN). In order to compare the privacy leak behavior among different software, we further propose a comprehensive metric, namely, overall leak degree, based on these four metrics. Finally, we validate the effectiveness of the proposed approach using real-world software applications. The experimental results demonstrate that our approach can quantitatively analyze the privacy leak behaviors of various software types and reveal their characteristics from different aspects.

FAME, a microprocessor based front-end analysis and modeling environment

NASA Technical Reports Server (NTRS)

Rosenbaum, J. D.; Kutin, E. B.

1980-01-01

Higher order software (HOS) is a methodology for the specification and verification of large scale, complex, real time systems. The HOS methodology was implemented as FAME (front end analysis and modeling environment), a microprocessor based system for interactively developing, analyzing, and displaying system models in a low cost user-friendly environment. The nature of the model is such that when completed it can be the basis for projection to a variety of forms such as structured design diagrams, Petri-nets, data flow diagrams, and PSL/PSA source code. The user's interface with the analyzer is easily recognized by any current user of a structured modeling approach; therefore extensive training is unnecessary. Furthermore, when all the system capabilities are used one can check on proper usage of data types, functions, and control structures thereby adding a new dimension to the design process that will lead to better and more easily verified software designs.

Input-output identification of controlled discrete manufacturing systems

NASA Astrophysics Data System (ADS)

Estrada-Vargas, Ana Paula; López-Mellado, Ernesto; Lesage, Jean-Jacques

2014-03-01

The automated construction of discrete event models from observations of external system's behaviour is addressed. This problem, often referred to as system identification, allows obtaining models of ill-known (or even unknown) systems. In this article, an identification method for discrete event systems (DESs) controlled by a programmable logic controller is presented. The method allows processing a large quantity of observed long sequences of input/output signals generated by the controller and yields an interpreted Petri net model describing the closed-loop behaviour of the automated DESs. The proposed technique allows the identification of actual complex systems because it is sufficiently efficient and well adapted to cope with both the technological characteristics of industrial controllers and data collection requirements. Based on polynomial-time algorithms, the method is implemented as an efficient software tool which constructs and draws the model automatically; an overview of this tool is given through a case study dealing with an automated manufacturing system.

A computer architecture for intelligent machines

NASA Technical Reports Server (NTRS)

Lefebvre, D. R.; Saridis, G. N.

1991-01-01

The Theory of Intelligent Machines proposes a hierarchical organization for the functions of an autonomous robot based on the Principle of Increasing Precision With Decreasing Intelligence. An analytic formulation of this theory using information-theoretic measures of uncertainty for each level of the intelligent machine has been developed in recent years. A computer architecture that implements the lower two levels of the intelligent machine is presented. The architecture supports an event-driven programming paradigm that is independent of the underlying computer architecture and operating system. Details of Execution Level controllers for motion and vision systems are addressed, as well as the Petri net transducer software used to implement Coordination Level functions. Extensions to UNIX and VxWorks operating systems which enable the development of a heterogeneous, distributed application are described. A case study illustrates how this computer architecture integrates real-time and higher-level control of manipulator and vision systems.

Rotational Motion of Axisymmetric Marangoni Swimmers

NASA Astrophysics Data System (ADS)

Rothstein, Jonathan; Uvanovic, Nick

2017-11-01

A series of experiments will be presented investigating the motion of millimeter-sized particles on the surface of water. The particles were partially coated with ethanol and carefully placed on a water interface in a series of Petri dishes with different diameters. High speed particle motion was driven by strong surface tension gradients as the ethanol slowly diffuses from the particles into the water resulting in a Marangoni flow. The velocity and acceleration of the particles where measured. In addition to straight line motion, the presence of the bounding walls of the circular Petri dish was found to induce an asymmetric, rotational motion of the axisymmetric Marangoni swimmers. The rotation rate and radius of curvature was found to be a function of the size of the Petri dish and the curvature of the air-water interface near the edge of the dish. For large Petri dishes or small particles, rotation motion was observed far from the bounding walls. In these cases, the symmetry break appears to be the result of the onset of votex shedding. Finally, multiple spherical particles were observed to undergo assembly driven by capillary forces followed by explosive disassembly.

Simulation-based model checking approach to cell fate specification during Caenorhabditis elegans vulval development by hybrid functional Petri net with extension.

PubMed

Li, Chen; Nagasaki, Masao; Ueno, Kazuko; Miyano, Satoru

2009-04-27

Model checking approaches were applied to biological pathway validations around 2003. Recently, Fisher et al. have proved the importance of model checking approach by inferring new regulation of signaling crosstalk in C. elegans and confirming the regulation with biological experiments. They took a discrete and state-based approach to explore all possible states of the system underlying vulval precursor cell (VPC) fate specification for desired properties. However, since both discrete and continuous features appear to be an indispensable part of biological processes, it is more appropriate to use quantitative models to capture the dynamics of biological systems. Our key motivation of this paper is to establish a quantitative methodology to model and analyze in silico models incorporating the use of model checking approach. A novel method of modeling and simulating biological systems with the use of model checking approach is proposed based on hybrid functional Petri net with extension (HFPNe) as the framework dealing with both discrete and continuous events. Firstly, we construct a quantitative VPC fate model with 1761 components by using HFPNe. Secondly, we employ two major biological fate determination rules - Rule I and Rule II - to VPC fate model. We then conduct 10,000 simulations for each of 48 sets of different genotypes, investigate variations of cell fate patterns under each genotype, and validate the two rules by comparing three simulation targets consisting of fate patterns obtained from in silico and in vivo experiments. In particular, an evaluation was successfully done by using our VPC fate model to investigate one target derived from biological experiments involving hybrid lineage observations. However, the understandings of hybrid lineages are hard to make on a discrete model because the hybrid lineage occurs when the system comes close to certain thresholds as discussed by Sternberg and Horvitz in 1986. Our simulation results suggest that: Rule I that cannot be applied with qualitative based model checking, is more reasonable than Rule II owing to the high coverage of predicted fate patterns (except for the genotype of lin-15ko; lin-12ko double mutants). More insights are also suggested. The quantitative simulation-based model checking approach is a useful means to provide us valuable biological insights and better understandings of biological systems and observation data that may be hard to capture with the qualitative one.

Modeling integrated cellular machinery using hybrid Petri-Boolean networks.

PubMed

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models.

Modeling Integrated Cellular Machinery Using Hybrid Petri-Boolean Networks

PubMed Central

Berestovsky, Natalie; Zhou, Wanding; Nagrath, Deepak; Nakhleh, Luay

2013-01-01

The behavior and phenotypic changes of cells are governed by a cellular circuitry that represents a set of biochemical reactions. Based on biological functions, this circuitry is divided into three types of networks, each encoding for a major biological process: signal transduction, transcription regulation, and metabolism. This division has generally enabled taming computational complexity dealing with the entire system, allowed for using modeling techniques that are specific to each of the components, and achieved separation of the different time scales at which reactions in each of the three networks occur. Nonetheless, with this division comes loss of information and power needed to elucidate certain cellular phenomena. Within the cell, these three types of networks work in tandem, and each produces signals and/or substances that are used by the others to process information and operate normally. Therefore, computational techniques for modeling integrated cellular machinery are needed. In this work, we propose an integrated hybrid model (IHM) that combines Petri nets and Boolean networks to model integrated cellular networks. Coupled with a stochastic simulation mechanism, the model simulates the dynamics of the integrated network, and can be perturbed to generate testable hypotheses. Our model is qualitative and is mostly built upon knowledge from the literature and requires fine-tuning of very few parameters. We validated our model on two systems: the transcriptional regulation of glucose metabolism in human cells, and cellular osmoregulation in S. cerevisiae. The model produced results that are in very good agreement with experimental data, and produces valid hypotheses. The abstract nature of our model and the ease of its construction makes it a very good candidate for modeling integrated networks from qualitative data. The results it produces can guide the practitioner to zoom into components and interconnections and investigate them using such more detailed mathematical models. PMID:24244124

Does incineration turn infectious waste aseptic?

PubMed

Kanemitsu, K; Inden, K; Kunishima, H; Ueno, K; Hatta, M; Gunji, Y; Watanabe, I; Kaku, M

2005-08-01

Incineration of infectious waste is considered to be biologically safe. We performed basic experiments to confirm that bacillus spores are killed by incineration in a muffle furnace. Biological samples containing 10(6) spores of Bacillus stearothermophilus were placed in stainless steel Petri dishes and then into hot furnaces. The furnace temperature and duration of incineration were 300 degrees C for 15 min, 300 degrees C for 30 min, 500 degrees C for 15 min, 500 degrees C for 30 min and 1100 degrees C for 3 min. We confirmed that all spores of B. stearothermophilus were killed at each of these settings. The effect of incineration seems to be equivalent to that of sterilization, based on the satisfactory sterilization assurance level of 10(-6).

TRI.NET Tutorial with Examples

EPA Pesticide Factsheets

This tutorial walks users through some sample TRI.NET searches to illustrate some of the ways this application can be used to access TRI data and answer basic questions about toxic chemical releases in a specific geographic area.

In Italy, a Partisan Defender of Foreign Professors

ERIC Educational Resources Information Center

Rocca, Francis X.

2007-01-01

Over the past quarter-century David Petrie, a 56-year-old Scotsman has attended, in the capacity of plaintiff or interested observer, at least 80 court hearings at various levels of the Italian and pan-European judicial systems--all in cases of alleged job discrimination by Italian universities. In the process, Mr. Petrie has become the public…

Father Google and Mother IM: Confessions of a Net Gen Learner

ERIC Educational Resources Information Center

Windham, Carie

2005-01-01

To bridge the technology cultural gap between many faculty and administrators and the youngest generation of college students, this author, a recent graduate, reveals what being a "Net Gener" really means and how that can translate to the classroom. She discusses what she considers the basic principles that guide the Net Generation: (1)…

WheelchairNet

MedlinePlus

... Basic training led by Padmaja Kankipati in Bangalore, India, May-June 2016 Participants at ISWP Hybrid-Basic training class, led by Padmaja Kankipati, SMOI, Bangalore, India, May-June 2016 ISWP Research and Training Coordinator ...

Safety of MRI with metallic middle ear implants.

PubMed

Tohme, Souheil M; Karkas, Alexandre A; Romanos, Bassam H

2003-01-01

Investigation of the effects of magnetic resonance fields on commonly used metallic middle ear implants. Nine middle ear prostheses (seven containing stainless steel and two made of pure gold used as control) were tested in vitro and one stainless steel stapedectomy prosthesis was tested on a cadaveric temporal bone. Each metallic prosthesis was placed in an empty Petri dish and introduced into a 1.5-tesla (T) magnetic resonance imaging (MRI) unit. Most of the prostheses were then placed in a water-filled Petri dish and reintroduced into the MRI unit. Eventual in vitro displacement was assessed visually by two means. In situ testing was done by implanting a piston in a cadaveric temporal bone and performing MR sequences ; any possible displacement was then assessed by CT scan and under microscopic vision. None of the prostheses was displaced in the empty Petri dish. However, while in the water-filled Petri dish, three of these moved with the flux. The implanted piston in the temporal bone did not move. The displacement of three of the prostheses in water is not relevant in real clinical situations. MRI can thus be considered safe in usual clinical settings, as far as our studied implants are concerned.

STS-93 MS Tognini checks the BRIC experiment petri dishes on the middeck

NASA Image and Video Library

2013-11-18

STS093-350-008 (22-27 July 1999) --- Astronaut Michel Tognini, mission specialist representing France’s Centre National d’Etudes Spatiales (CNES), checks the Biological Research in Canisters (BRIC) payload petri dishes on the mid deck of the Space Shuttle Columbia. BRIC was designed to investigate the effects of space flight on small arthropod animals and plant specimens.

Software-Based Visual Loan Calculator For Banking Industry

NASA Astrophysics Data System (ADS)

Isizoh, A. N.; Anazia, A. E.; Okide, S. O. 3; Onyeyili, T. I.; Okwaraoka, C. A. P.

2012-03-01

industry is very necessary in modern day banking system using many design techniques for security reasons. This paper thus presents the software-based design and implementation of a Visual Loan calculator for banking industry using Visual Basic .Net (VB.Net). The fundamental approach to this is to develop a Graphical User Interface (GUI) using VB.Net operating tools, and then developing a working program which calculates the interest of any loan obtained. The VB.Net programming was done, implemented and the software proved satisfactory.

Mechanisms and disease relevance of neutrophil extracellular trap formation.

PubMed

Van Avondt, Kristof; Hartl, Dominik

2018-03-15

While the microscopic appearance of neutrophil extracellular traps (NETs) has fascinated basic researchers since its discovery, the (patho)physiological mechanisms triggering NET release, the disease relevance and clinical translatability of this unconventional cellular mechanism remained poorly understood. Here, we summarize and discuss current concepts of the mechanisms and disease relevance of NET formation. © 2018 Stichting European Society for Clinical Investigation Journal Foundation.

Building a better sticky trap: description of an easy-to-use trap and pole mount for quantifying the abundance of adult aquatic insects

USGS Publications Warehouse

Smith, Joshua T.; Kennedy, Theodore A.; Muehlbauer, Jeffrey D.

2014-01-01

Insect emergence is a fundamental process in freshwaters. It is a critical life-history stage for aquatic insects and provides an important prey resource for terrestrial and aquatic consumers. Sticky traps are increasingly being used to sample these insects. The most common design consists of an acetate sheet coated with a nondrying adhesive that is attached to a wire frame or cylinder. These traps must be prepared at the deployment site, a process that can be time consuming and difficult given the vagaries of field conditions. Our goals were to develop a sturdy, low-cost sticky trap that could be prepared in advance, rapidly deployed and recovered in the field, and used to estimate the flight direction of insects. We used 150-mm Petri dishes with lids. The dishes can be coated cleanly and consistently with Tangle-Trap® adhesive. Deploying traps is simple and requires only a pole set near the body of water being sampled. Four dishes can be attached to the pole using Velcro and aligned in 4 different directions to enable quantification of insect flight direction. After sampling, Petri dishes can be taped closed, packed in boxes, and stored indefinitely. Petri traps are comparable in price to standard acetate sheet traps at ∼US$0.50/directional deployment, but they require more space for storage than acetate sheet traps. However, a major benefit of Petri traps is that field deployment times are ⅓ those of acetate traps. Our study demonstrated that large Petri dishes are an ideal platform for sampling postemergent adult aquatic insects, particularly when the study design involves estimating flight direction and when rapid deployment and recovery of traps is critical.

Operational characterisation of requirements and early validation environment for high demanding space systems

NASA Technical Reports Server (NTRS)

Barro, E.; Delbufalo, A.; Rossi, F.

1993-01-01

The definition of some modern high demanding space systems requires a different approach to system definition and design from that adopted for traditional missions. System functionality is strongly coupled to the operational analysis, aimed at characterizing the dynamic interactions of the flight element with its surrounding environment and its ground control segment. Unambiguous functional, operational and performance requirements are to be defined for the system, thus improving also the successive development stages. This paper proposes a Petri Nets based methodology and two related prototype applications (to ARISTOTELES orbit control and to Hermes telemetry generation) for the operational analysis of space systems through the dynamic modeling of their functions and a related computer aided environment (ISIDE) able to make the dynamic model work, thus enabling an early validation of the system functional representation, and to provide a structured system requirements data base, which is the shared knowledge base interconnecting static and dynamic applications, fully traceable with the models and interfaceable with the external world.

Formal Verification of the Runway Safety Monitor

NASA Technical Reports Server (NTRS)

Siminiceanu, Radu; Ciardo, Gianfranco

2006-01-01

The Runway Safety Monitor (RSM) designed by Lockheed Martin is part of NASA's effort to reduce runway accidents. We developed a Petri net model of the RSM protocol and used the model checking functions of our tool SMART to investigate a number of safety properties in RSM. To mitigate the impact of state-space explosion, we built a highly discretized model of the system, obtained by partitioning the monitored runway zone into a grid of smaller volumes and by considering scenarios involving only two aircraft. The model also assumes that there are no communication failures, such as bad input from radar or lack of incoming data, thus it relies on a consistent view of reality by all participants. In spite of these simplifications, we were able to expose potential problems in the RSM conceptual design. Our findings were forwarded to the design engineers, who undertook corrective action. Additionally, the results stress the efficiency attained by the new model checking algorithms implemented in SMART, and demonstrate their applicability to real-world systems.

Multi-agent Simulations of Population Behavior: A Promising Tool for Systems Biology.

PubMed

Colosimo, Alfredo

2018-01-01

This contribution reports on the simulation of some dynamical events observed in the collective behavior of different kinds of populations, ranging from shape-changing cells in a Petri dish to functionally correlated brain areas in vivo. The unifying methodological approach, based upon a Multi-Agent Simulation (MAS) paradigm as incorporated in the NetLogo™ interpreter, is a direct consequence of the cornerstone that simple, individual actions within a population of interacting agents often give rise to complex, collective behavior.The discussion will mainly focus on the emergence and spreading of synchronous activities within the population, as well as on the modulation of the collective behavior exerted by environmental force-fields. A relevant section of this contribution is dedicated to the extension of the MAS paradigm to Brain Network models. In such a general framework some recent applications taken from the direct experience of the author, and exploring the activation patterns characteristic of specific brain functional states, are described, and their impact on the Systems-Biology universe underlined.

Influence of oxygen on the chemical stage of radiobiological mechanism

NASA Astrophysics Data System (ADS)

Barilla, Jiří; Lokajíček, Miloš V.; Pisaková, Hana; Simr, Pavel

2016-07-01

The simulation of the chemical stage of radiobiological mechanism may be very helpful in studying the radiobiological effect of ionizing radiation when the water radical clusters formed by the densely ionizing ends of primary or secondary charged particle may form DSBs damaging DNA molecules in living cells. It is possible to study not only the efficiency of individual radicals but also the influence of other species or radiomodifiers (mainly oxygen) being present in water medium during irradiation. The mathematical model based on Continuous Petri nets (proposed by us recently) will be described. It makes it possible to analyze two main processes running at the same time: chemical radical reactions and the diffusion of radical clusters formed during energy transfer. One may study the time change of radical concentrations due to the chemical reactions running during diffusion process. Some orientation results concerning the efficiency of individual radicals in DSB formation (in the case of Co60 radiation) will be presented; the influence of oxygen present in water medium during irradiation will be shown, too.

Aligning observed and modelled behaviour based on workflow decomposition

NASA Astrophysics Data System (ADS)

Wang, Lu; Du, YuYue; Liu, Wei

2017-09-01

When business processes are mostly supported by information systems, the availability of event logs generated from these systems, as well as the requirement of appropriate process models are increasing. Business processes can be discovered, monitored and enhanced by extracting process-related information. However, some events cannot be correctly identified because of the explosion of the amount of event logs. Therefore, a new process mining technique is proposed based on a workflow decomposition method in this paper. Petri nets (PNs) are used to describe business processes, and then conformance checking of event logs and process models is investigated. A decomposition approach is proposed to divide large process models and event logs into several separate parts that can be analysed independently; while an alignment approach based on a state equation method in PN theory enhances the performance of conformance checking. Both approaches are implemented in programmable read-only memory (ProM). The correctness and effectiveness of the proposed methods are illustrated through experiments.

Development of a Rotary Wing Unmanned Aerial Vehicle (UAV) Simulation Model

DTIC Science & Technology

2014-03-01

Features Language URL Autopilot: DIY UAV - 2 DOF proportional controller - Kalman filtering C http://autopilot.sour ceforge.net Paperazzi - 3 DOF...proprtional controller - Basic navigation OCaml http://paparazzi.ena c.fr JSBSim - Basic control system blockset - Sample autopilot

WaveNet: A Web-Based Metocean Data Access, Processing, and Analysis Tool. Part 3 - CDIP Database

DTIC Science & Technology

2014-06-01

and Analysis Tool; Part 3 – CDIP Database by Zeki Demirbilek, Lihwa Lin, and Derek Wilson PURPOSE: This Coastal and Hydraulics Engineering...Technical Note (CHETN) describes coupling of the Coastal Data Information Program ( CDIP ) database to WaveNet, the first module of MetOcnDat (Meteorological...provides a step-by-step procedure to access, process, and analyze wave and wind data from the CDIP database. BACKGROUND: WaveNet addresses a basic

Net current control device. Final report

DOE Office of Scientific and Technical Information (OSTI.GOV)

Fugate, D.; Cooper, J.H.

1998-11-01

Net currents generally result in elevated magnetic fields because the alternate paths are distant from the circuit conductors. Investigations have shown that one of the primary sources of power frequency magnetic fields in residential buildings is currents that return to their source via paths other than the neutral conductors. As part of EPRI`s Magnetic Field Shielding Project, ferromagnetic devices, called net current control (NCC) devices, were developed and tested for use in reducing net currents on electric power cables and the resulting magnetic fields. Applied to a residential service drop, an NCC device reduces net current by forcing current offmore » local non-utility ground paths, and back onto the neutral conductor. Circuit models and basic design equations for the NCC concept were developed, and proof-of-principles tests were carried out on an actual residence with cooperation from the local utility. After proving the basic concepts, three prototype NCC devices were built and tested on a simulated neighborhood power system. Additional prototypes were built for testing by interested EPRI utility members. Results have shown that the NCC prototypes installed on residential service drops reduce net currents to milliampere levels with compromising the safety of the ground system. Although the focus was on application to residential service cables, the NCC concept is applicable to single-phase and three-phase distribution systems as well.« less

Comparison of functional assays used in the clinical development of a placental malaria vaccine.

PubMed

Pehrson, Caroline; Heno, Kristine K; Adams, Yvonne; Resende, Mafalda; Mathiesen, Line; Soegaard, Max; de Jongh, Willem A; Theander, Thor G; Salanti, Ali; Nielsen, Morten A

2017-01-23

Malaria in pregnancy is associated with significant morbidity in pregnant women and their offspring. Plasmodium falciparum infected erythrocytes (IE) express VAR2CSA that mediates binding to chondroitin sulphate A (CSA) in the placenta. Two VAR2CSA-based vaccines for placental malaria are in clinical development. The purpose of this study was to evaluate the robustness and comparability of binding inhibition assays used in the clinical development of placental malaria vaccines. The ability of sera from animals immunised with different VAR2CSA constructs to inhibit IE binding to CSA was investigated in three in vitro assays using 96-well plates, petri dishes, capillary flow and an ex vivo placental perfusion assay. The inter-assay variation was not uniform between assays and ranged from above ten-fold in the flow assay to two-fold in the perfusion assay. The intra-assay variation was highest in the petri dish assay. A positive correlation between IE binding avidity and the level of binding after antibody inhibition in the petri dish assay indicate that high avidity IE binding is more difficult to inhibit. The highest binding inhibition sensitivity was found in the 96-well and petri dish assays compared to the flow and perfusion assays where binding inhibition required higher antibody titers. The inhibitory capacity of antibodies is not easily translated between assays and the high sensitivity of the 96-well and petri dish assays stresses the need for comparing serial dilutions of serum. Furthermore, IE binding avidity must be in the same range when comparing data from different days. There was an overall concordance in the capacity of antibody-mediated inhibition, when comparing the in vitro assays with the perfusion assay, which more closely represents in vivo conditions. Importantly the ID1-ID2a protein in a liposomal formulation, currently in a phase I trial, effectively induced antibodies that inhibited IE adhesion in placental tissue. Copyright © 2016. Published by Elsevier Ltd.

CAMUS: Automatically Mapping Cyber Assets to Mission and Users (PREPRINT)

DTIC Science & Technology

2009-10-01

which machines regularly use a particular mail server. Armed with these basic data sources – LDAP, NetFlow traffic and user logs – fuselets were created... NetFlow traffic used in the demonstration has over ten thousand unique IP Addresses and is over one gigabyte in size. A number of high performance

[Chemotherapy for GI and pancreatic NETs].

PubMed

Doi, Toshihiko

2013-07-01

Neuroendocrine tumors(NETs)describe a heterogeneous group of tumors with a wide range of morphologic, functional, and behavioral characteristics. Pancreatic neuroendocrine tumors(pNET)are a subset of NETs which are increasing in incidence and prevalence. These tumors are generally slow growing and behave in an indolent fashion. However, when these tumors spread they can be life threatening and difficult to treat with current modalities. Recently, the basic treatment for pNET was changed with the approval of two targeted agents, sunitinib and everolimus. Clinical trials conducting various combinations of somatostatin analogues, mTOR inhibitors, tyrosine kinase inhibitors, and cytotoxic agents are ongoing under-evaluation, and a multitargeted approach to therapy will translate into improved patient outcomes.

Testing of Compounds for Efficacy against Schistosomiasis.

DTIC Science & Technology

1987-08-25

Nostoc muscorU) has been grown (Liang, 1974) is placed in all glass aquaria, and plastic trays to serve as an additional food source. Snails in petri...supplemented with blue-green algae ( Nostoc muscoru) and mud forms the diet of stock snails in glass aquaria as well as those kept in plastic trays. The agar...green algae ( Nostoc muscorum) and water is used for rearing young * snails and maintaining both pre-patent and patent snails V (Liang, 1974); 3) a petri

How Online Basic Psychological Need Satisfaction Influences Self-Disclosure Online among Chinese Adolescents: Moderated Mediation Effect of Exhibitionism and Narcissism.

PubMed

Liu, Ying; Liu, Ru-De; Ding, Yi; Wang, Jia; Zhen, Rui; Xu, Le

2016-01-01

Under the basic framework of self-determination theory, the present study examined a moderated mediation model in which exhibitionism mediated the relationship between online basic psychological need satisfaction and self-disclosure on the mobile Internet, and this mediation effect was moderated by narcissism. A total of 296 Chinese middle school students participated in this research. The results revealed that exhibitionism fully mediated the association between online competence need satisfaction and self-disclosure on the mobile net, and partly mediated the association between online relatedness need satisfaction and self-disclosure on the mobile net. The mediating path from online basic psychological need satisfaction (competence and relatedness) to exhibitionism was moderated by narcissism. Compared to the low level of narcissism, online competence need satisfaction had a stronger predictive power on exhibitionism under the high level of narcissism condition. In contrast, online relatedness need satisfaction had a weaker predictive power on exhibitionism.

How Online Basic Psychological Need Satisfaction Influences Self-Disclosure Online among Chinese Adolescents: Moderated Mediation Effect of Exhibitionism and Narcissism

PubMed Central

Liu, Ying; Liu, Ru-De; Ding, Yi; Wang, Jia; Zhen, Rui; Xu, Le

2016-01-01

Under the basic framework of self-determination theory, the present study examined a moderated mediation model in which exhibitionism mediated the relationship between online basic psychological need satisfaction and self-disclosure on the mobile Internet, and this mediation effect was moderated by narcissism. A total of 296 Chinese middle school students participated in this research. The results revealed that exhibitionism fully mediated the association between online competence need satisfaction and self-disclosure on the mobile net, and partly mediated the association between online relatedness need satisfaction and self-disclosure on the mobile net. The mediating path from online basic psychological need satisfaction (competence and relatedness) to exhibitionism was moderated by narcissism. Compared to the low level of narcissism, online competence need satisfaction had a stronger predictive power on exhibitionism under the high level of narcissism condition. In contrast, online relatedness need satisfaction had a weaker predictive power on exhibitionism. PMID:27616999

A Software Agent Toolkit for Effective Information Processing in the Battle Command Domain

DTIC Science & Technology

2006-11-01

the ADE will be based on a popular Integrated Development Environment (IDE) such as NetBeans or Eclipse. We further specified that the IDE is to be...JBuilder, NetBeans , and Eclipse. We quickly eliminated Visual Studio and JBuilder because they did not meet our basic requirements of being Java...based and freely obtainable. This left us with NetBeans and Eclipse. Each is a solid IDE with features that permit extensions well suited to our

Working towards an international consensus on criteria for assessing internet gaming disorder: a critical commentary on Petry et al. (2014)

PubMed Central

GRIFFITHS, MARK D.; VAN ROOIJ, ANTONIUS J.; KARDEFELT-WINTHER, DANIEL; STARCEVIC, VLADAN; KIRÁLY, ORSOLYA; PALLESEN, STÅLE; MÜLLER, KAI; DREIER, MICHAEL; CARRAS, MICHELLE; PRAUSE, NICOLE; KING, DANIEL L.; ABOUJAOUDE, ELLIAS; KUSS, DARIA J.; PONTES, HALLEY M.; FERNANDEZ, OLATZ LOPEZ; NAGYGYORGY, KATALIN; ACHAB, SOPHIA; BILLIEUX, JOËL; QUANDT, THORSTEN; CARBONELL, XAVIER; FERGUSON, CHRISTOPHER J.; HOFF, RANI A.; DEREVENSKY, JEFFREY; HAAGSMA, MARIA C.; DELFABBRO, PAUL; COULSON, MARK; HUSSAIN, ZAHEER; DEMETROVICS, ZSOLT

2017-01-01

This commentary paper critically discusses the recent debate paper by Petry et al. (2014) that argued there was now an international consensus for assessing Internet Gaming Disorder (IGD). Our collective opinions vary considerably regarding many different aspects of online gaming. However, we contend that the paper by Petry and colleagues does not provide a true and representative international community of researchers in this area. This paper critically discusses and provides commentary on (i) the representativeness of the international group that wrote the ‘consensus’ paper, and (ii) each of the IGD criteria. The paper also includes a brief discussion on initiatives that could be taken to move the field towards consensus. It is hoped that this paper will foster debate in the IGD field and lead to improved theory, better methodologically designed studies, and more robust empirical evidence as regards problematic gaming and its psychosocial consequences and impact. PMID:26669530

Uncle Sam's Net of Knowledge for Schools.

ERIC Educational Resources Information Center

Kelly, Melody Specht

This book is a comprehensive guide to help school librarians and teachers find and make the best use of government information the new electronic environment. The first chapter "Internet Basics and Federal Information on the Web: An Introduction" shows how to get started by discussing Internet basics, document formats commonly used by…

Microscale Chemistry in a Plastic Petri Dish: Preparation and Chemical Properties of Chlorine Gas

NASA Astrophysics Data System (ADS)

Choi, Martin M. F.

2002-08-01

This experiment demonstrates some of the chemistry of chlorine on a microscale, about the size of a water droplet. Chlorine gas was prepared from an acidified bleach solution in a plastic petri dish. The chlorine gas generated in situ reacted with other chemical reagents in the dish by diffusion. Some of the oxidizing properties and bleaching power of chlorine gas were shown visually and could be observed within 10 minutes. These experiments provide suitable hands-on experience for students at secondary-school level.

Induction of trap formation in nematode-trapping fungi by bacteria-released ammonia.

PubMed

Su, H N; Xu, Y Y; Wang, X; Zhang, K Q; Li, G H

2016-04-01

A total of 11 bacterial strains were assayed for bacteria-induced trap formation in the nematode-trapping fungus Arthrobotrys oligospora YMF1·01883 with two-compartmented Petri dish. These strains were identified on the basis of their 16S rRNA gene sequences. Volatile organic compounds (VOCs) of eight isolates were extracted using solid-phase micro-extraction (SPME) and their structures were identified based on gas chromatography-mass spectrometry (GC-MS). At the same time, all isolates were used for quantitative measurement of ammonia by the indophenol blue method. The effects of pure commercial compounds on inducement of trap formation in A. oligospora were tested. Taken together, results demonstrated that the predominant bacterial volatile compound inducing trap formation was ammonia. Meanwhile, ammonia also played a role in other nematode-trapping fungi, including Arthrobotrys guizhouensis YMF1·00014, producing adhesive nets; Dactylellina phymatopaga YMF1·01474, producing adhesive knobs; Dactylellina cionopaga YMF1·01472, producing adhesive columns and Drechslerella brochopaga YMF1·01829, producing constricting rings. © 2016 The Society for Applied Microbiology.

Composing, Analyzing and Validating Software Models

NASA Astrophysics Data System (ADS)

Sheldon, Frederick T.

1998-10-01

This research has been conducted at the Computational Sciences Division of the Information Sciences Directorate at Ames Research Center (Automated Software Engineering Grp). The principle work this summer has been to review and refine the agenda that were carried forward from last summer. Formal specifications provide good support for designing a functionally correct system, however they are weak at incorporating non-functional performance requirements (like reliability). Techniques which utilize stochastic Petri nets (SPNs) are good for evaluating the performance and reliability for a system, but they may be too abstract and cumbersome from the stand point of specifying and evaluating functional behavior. Therefore, one major objective of this research is to provide an integrated approach to assist the user in specifying both functionality (qualitative: mutual exclusion and synchronization) and performance requirements (quantitative: reliability and execution deadlines). In this way, the merits of a powerful modeling technique for performability analysis (using SPNs) can be combined with a well-defined formal specification language. In doing so, we can come closer to providing a formal approach to designing a functionally correct system that meets reliability and performance goals.

Modeling and measurement of fault-tolerant multiprocessors

NASA Technical Reports Server (NTRS)

Shin, K. G.; Woodbury, M. H.; Lee, Y. H.

1985-01-01

The workload effects on computer performance are addressed first for a highly reliable unibus multiprocessor used in real-time control. As an approach to studing these effects, a modified Stochastic Petri Net (SPN) is used to describe the synchronous operation of the multiprocessor system. From this model the vital components affecting performance can be determined. However, because of the complexity in solving the modified SPN, a simpler model, i.e., a closed priority queuing network, is constructed that represents the same critical aspects. The use of this model for a specific application requires the partitioning of the workload into job classes. It is shown that the steady state solution of the queuing model directly produces useful results. The use of this model in evaluating an existing system, the Fault Tolerant Multiprocessor (FTMP) at the NASA AIRLAB, is outlined with some experimental results. Also addressed is the technique of measuring fault latency, an important microscopic system parameter. Most related works have assumed no or a negligible fault latency and then performed approximate analyses. To eliminate this deficiency, a new methodology for indirectly measuring fault latency is presented.

Function Allocation between Automation and Human Pilot for Airborne Separation Assurance

NASA Technical Reports Server (NTRS)

Idris, Husni; Enea, Gabriele; Lewis, TImothy A.

2016-01-01

Maintaining safe separation between aircraft is a key determinant of the airspace capacity to handle air transportation. With the advent of satellite-based surveillance, aircraft equipped with the needed technologies are now capable of maintaining awareness of their location in the airspace and sharing it with their surrounding traffic. As a result, concepts and cockpit automation are emerging to enable delegating the responsibility of maintaining safe separation from traffic to the pilot; thus increasing the airspace capacity by alleviating the limitation of the current non-scalable centralized ground-based system. In this paper, an analysis of allocating separation assurance functions to the human pilot and cockpit automation is presented to support the design of these concepts and technologies. A task analysis was conducted with the help of Petri nets to identify the main separation assurance functions and their interactions. Each function was characterized by three behavior levels that may be needed to perform the task: skill, rule and knowledge based levels. Then recommendations are made for allocating each function to an automation scale based on their behavior level characterization and with the help of Subject matter experts.

Composing, Analyzing and Validating Software Models

NASA Technical Reports Server (NTRS)

Sheldon, Frederick T.

1998-01-01

This research has been conducted at the Computational Sciences Division of the Information Sciences Directorate at Ames Research Center (Automated Software Engineering Grp). The principle work this summer has been to review and refine the agenda that were carried forward from last summer. Formal specifications provide good support for designing a functionally correct system, however they are weak at incorporating non-functional performance requirements (like reliability). Techniques which utilize stochastic Petri nets (SPNs) are good for evaluating the performance and reliability for a system, but they may be too abstract and cumbersome from the stand point of specifying and evaluating functional behavior. Therefore, one major objective of this research is to provide an integrated approach to assist the user in specifying both functionality (qualitative: mutual exclusion and synchronization) and performance requirements (quantitative: reliability and execution deadlines). In this way, the merits of a powerful modeling technique for performability analysis (using SPNs) can be combined with a well-defined formal specification language. In doing so, we can come closer to providing a formal approach to designing a functionally correct system that meets reliability and performance goals.

Experimental and theoretical studies of the thermal behavior of titanium dioxide-SnO2 based composites.

PubMed

Voga, G P; Coelho, M G; de Lima, G M; Belchior, J C

2011-04-07

In this paper we report experimental and theoretical studies concerning the thermal behavior of some organotin-Ti(IV) oxides employed as precursors for TiO(2)/SnO(2) semiconducting based composites, with photocatalytic properties. The organotin-TiO(2) supported materials were obtained by chemical reactions of SnBu(3)Cl (Bu = butyl), TiCl(4) with NH(4)OH in ethanol, in order to impregnate organotin oxide in a TiO(2) matrix. A theoretical model was developed to support experimental procedures. The kinetics parameters: frequency factor (A), activation energy, and reaction order (n) can be estimated through artificial intelligence methods. Genetic algorithm, fuzzy logic, and Petri neural nets were used in order to determine the kinetic parameters as a function of temperature. With this in mind, three precursors were prepared in order to obtain composites with Sn/TiO(2) ratios of 0% (1), 15% (2), and 30% (3) in weight, respectively. The thermal behavior of products (1-3) was studied by thermogravimetric experiments in oxygen.

Electro-Optical Inspection For Tolerance Control As An Integral Part Of A Flexible Machining Cell

NASA Astrophysics Data System (ADS)

Renaud, Blaise

1986-11-01

Institut CERAC has been involved in optical metrology and 3-dimensional surface control for the last couple of years. Among the industrial applications considered is the on-line shape evaluation of machined parts within the manufacturing cell. The specific objective is to measure the machining errors and to compare them with the tolerances set by designers. An electro-optical sensing technique has been developed which relies on a projection Moire contouring optical method. A prototype inspection system has been designed, making use of video detection and computer image processing. Moire interferograms are interpreted, and the metrological information automatically retrieved. A structured database can be generated for subsequent data analysis and for real-time closed-loop corrective actions. A real-time kernel embedded into a synchronisation network (Petri-net) for the control of concurrent processes in the Electra-Optical Inspection (E0I) station was realised and implemented in a MODULA-2 program DIN01. The prototype system for on-line automatic tolerance control taking place within a flexible machining cell is described in this paper, together with the fast-prototype synchronisation program.

Computational Systems Biology in Cancer: Modeling Methods and Applications

PubMed Central

Materi, Wayne; Wishart, David S.

2007-01-01

In recent years it has become clear that carcinogenesis is a complex process, both at the molecular and cellular levels. Understanding the origins, growth and spread of cancer, therefore requires an integrated or system-wide approach. Computational systems biology is an emerging sub-discipline in systems biology that utilizes the wealth of data from genomic, proteomic and metabolomic studies to build computer simulations of intra and intercellular processes. Several useful descriptive and predictive models of the origin, growth and spread of cancers have been developed in an effort to better understand the disease and potential therapeutic approaches. In this review we describe and assess the practical and theoretical underpinnings of commonly-used modeling approaches, including ordinary and partial differential equations, petri nets, cellular automata, agent based models and hybrid systems. A number of computer-based formalisms have been implemented to improve the accessibility of the various approaches to researchers whose primary interest lies outside of model development. We discuss several of these and describe how they have led to novel insights into tumor genesis, growth, apoptosis, vascularization and therapy. PMID:19936081

A compositional framework for reaction networks

NASA Astrophysics Data System (ADS)

Baez, John C.; Pollard, Blake S.

Reaction networks, or equivalently Petri nets, are a general framework for describing processes in which entities of various kinds interact and turn into other entities. In chemistry, where the reactions are assigned ‘rate constants’, any reaction network gives rise to a nonlinear dynamical system called its ‘rate equation’. Here we generalize these ideas to ‘open’ reaction networks, which allow entities to flow in and out at certain designated inputs and outputs. We treat open reaction networks as morphisms in a category. Composing two such morphisms connects the outputs of the first to the inputs of the second. We construct a functor sending any open reaction network to its corresponding ‘open dynamical system’. This provides a compositional framework for studying the dynamics of reaction networks. We then turn to statics: that is, steady state solutions of open dynamical systems. We construct a ‘black-boxing’ functor that sends any open dynamical system to the relation that it imposes between input and output variables in steady states. This extends our earlier work on black-boxing for Markov processes.

Automatic Response to Intrusion

DTIC Science & Technology

2002-10-01

Computing Corporation Sidewinder Firewall [18] SRI EMERALD Basic Security Module (BSM) and EMERALD File Transfer Protocol (FTP) Monitors...the same event TCP Wrappers [24] Internet Security Systems RealSecure [31] SRI EMERALD IDIP monitor NAI Labs Generic Software Wrappers Prototype...included EMERALD , NetRadar, NAI Labs UNIX wrappers, ARGuE, MPOG, NetRadar, CyberCop Server, Gauntlet, RealSecure, and the Cyber Command System

Professional Development Capacity Building in Pennsylvania's Regional Staff Development Program: The "WorkNet" Project. Final Report [and] WorkNet Workplace Literacy Trainer's Guide.

ERIC Educational Resources Information Center

Carman, Priscilla S.

These two documents are products of a project to improve the capability of the Pennsylvania Regional Staff Development Centers to provide current, research-based workplace literacy training and technical assistance to adult basic and literacy education programs. The final report describes these project activities: development of training materials…

Efficacy of entomopathogenic nematode Steinernema feltiae (Rhabditida: Steinernematidae) as influenced by Frankliniella occidentalis (Thysanoptera: Thripidae) developmental stage and host plant stage.

PubMed

Buitenhuis, R; Shipp, J L

2005-10-01

Entomopathogenic nematodes were investigated as an alternative biological control strategy for western flower thrips, Frankliniella occidentalis (Pergande) (Thysanoptera: Thripidae), in ornamental greenhouse crops, by using potted chrysanthemum as a model crop. The susceptibility of various life stages of F. occidentalis to different concentrations of the nematode Steinernema feltiae (Filipjev) (Rhabditida: Steinernematidae) was investigated in petri dish bioassays. This was followed with trials using potted chrysanthemums comparing the efficacy of nematode application to plants in vegetative (exposed habitat) versus flowering (cryptic habitat) stages. In both trials, the effect of the wetting agent Agral 90 (nonylphenoxy polyethoxyethanol), which is used in combination with the nematode spray, on F. occidentalis mortality was assessed. In petri dish trials, the prepupae and pupae were the most susceptible developmental stages of F. occidentalis to infection by S. feltiae. First and second instars were killed by very high rates of nematodes (> or =20,000 infective juveniles per milliliter), but corrected mortality was only approximately 28-37%. No significant mortality was observed for adult thrips. Results from the petri dish trials were confirmed on chrysanthemum plants. Foliar application of S. feltiae did not result in significant mortality in larvae or adults. No significant differences in efficacy were detected by application of nematodes on vegetative versus flowering chrysanthemum. Agral 90 had a significant impact on mortality on the first stage larvae and prepupae in the petri dish trials but not in the plant trials. Thrips control by S. feltiae in greenhouses may be partly or completely due to prepupal and pupal mortality.

Field measurements of dry deposition to spruce foliage and petri dishes in the Black Forest, F.R.G.

USGS Publications Warehouse

Shanley, J.B.

1989-01-01

Dry deposition fluxes Ca2+, Mg2+, K+, Mn2+, Pb2+ and SO42- to spruce foliage and petri dishes were measured in two high-elevation sites (>900 m) in the southern Black Forest, F.R.G., during 12 periods (2-7 days, each) from mid-September to mid-November, 1983, In situ extraction of deposited material from small spruce branches allowed repeated use of the same foliar collecting surfaces for a direct comparison of deposition between periods. Fluxes were corrected for leaching of internally cycled constituents using factors determined from serial extraction experiments. The ratio of flux to petri dishes vs foliage (P/F) was >1.0 for Ca2+, Pb2+ and SO42-, and somewhat 900 m) in the southern Black Forest, F.R.G., during 12 periods (2-7 days, each) from mid-September to mid-November, 1983. The ratio of flux to petri dishes vs foliage (P/F) was >1.0 for Ca2+, Pb2+, and SO42-, and somewhat <1.0 but more constant for Mg2+. Temporal variations in dry deposition fluxes at an exposed site near the industrialized Rhine Valley correlated with variations in total air particulate concentrations at a nearby air quality station. Deposition rates were comparable in magnitude but different in temporal pattern at a remote site in the Black Forest interior. Fluxes at each site reached a minimum during the period of 4-9 November when a regional air inversion confined pollutants to the Rhine Valley below the study sites. High fluxes accompanied the inversion break-up.

Calculations of the Acceleration of Centrifugal Loading on Adherent Cells

NASA Astrophysics Data System (ADS)

Chen, Kang; Song, Yang; Liu, Qing; Zhang, Chunqiu

2017-07-01

Studies have shown that the morphology and function of living cells are greatly affected by the state of different high acceleration. Based on the centrifuge, we designed a centrifugal cell loading machine for the mechanical biology of cells under high acceleration loading. For the machine, the feasibility of the experiment was studied by means of constant acceleration or variable acceleration loading in the Petri dish fixture and/or culture flask. Here we analyzed the distribution of the acceleration of the cells with the change of position and size of the culturing device quantitatively. It is obtained that Petri dish fixture and/or culture flask can be used for constant acceleration loading by experiments; the centripetal acceleration of the adherent cells increases with the increase of the distance between the rotor center of the centrifuge and the fixture of the Petri dish and the size of the fixture. It achieves the idea that the general biology laboratory can conduct the study of mechanical biology at high acceleration. It also provides a basis for more accurate study of the law of high acceleration on mechanobiology of cells.

Effect of pH and calcium on short-term NO3- fluxes in roots of barley seedlings

NASA Technical Reports Server (NTRS)

Aslam, M.; Travis, R. L.; Huffaker, R. C.

1995-01-01

The effect of pH and Ca2+ on net NO3- uptake, influx, and efflux by intact roots of barley (Hordeum vulgare L.) seedlings was studied. Seedlings were induced with NO3- or NO2-. Net NO3- uptake and efflux, respectively, were determined by following its depletion from, and accumulation in, the external solution. Since roots of both uninduced and NO2(-)-induced seedlings contain little internal NO3- initial net uptake rates are equivalent to influx (M. Aslam, R.L. Travis, R.C. Huffaker [1994] Plant Physiol 106: 1293-1301). NO3-, uptake (influx) by these roots was little affected at acidic pH. In contrast, in NO3(-)-induced roots, which accumulate NO3-, net uptake rates decreased in response to acidic pH. Under these conditions, NO3- efflux was stimulated and was a function of root NO3- concentration. Conversely, at basic pH, NO3- uptake by NO3- and NO2(-)-induced and uninduced roots decreased, apparently because of the inhibition of influx. Calcium had little effect on NO3- uptake (influx) by NO2(-)-induced roots at either pH 3 or 6. However, in NO3(-)-induced roots, lack of Ca2+ at pH 3 significantly decreased net NO3- uptake and stimulated efflux. The results indicate that at acidic pH the decrease in net NO3- uptake is due to the stimulation of efflux, whereas at basic pH, it is due to the inhibition of influx.

Contemporary Records of the (1492) Ensisheim Fall

NASA Astrophysics Data System (ADS)

Levi, F. A.; Levi-Donati, G. R.

1992-07-01

On the occasion of the five-hundredth anniversary of the Ensisheim (LL6) stone (November 16, 1492), five rare documents on this fall are presented: 1) Anonymous, Annali del Convento di S. Domenico. (in Italian) Manuscript n. 1151, Biblioteca Com. "Augusta", Perugia. 2) Eusebii Pamphili C. (1570) Chronicon. Petri, Basilea. (in Latin). 3) Lycosthenes (Wolffhart) C. (1557) Prodigiorum ac ostentorum Chronicon. Petri, Basilea. (in Latin). 4) Sansovino F. (1582) Cronologia del Mondo. Salicato, Vinegia. (in Italian). 5) Schedel H. (1492) Liber Chronicarum cum figuris et ymagi(ni)bus ab inicio mu(n)di. Koberger, Nuremberga. (in Latin).

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

Drs. Rob Ferl and Anna-Lisa Paul in a cold room in the Kennedy Space Center Processing Facility with the petri plates they prepped at the University of Florida for APEX-04. Paul is the principal investigator (PI) and Ferl is co-PI. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Statistical Match of the VA 1979-1980 Recipient File against the 1979-1980 Basic Grant Recipient File. Revised.

ERIC Educational Resources Information Center

Applied Management Sciences, Inc., Silver Spring, MD.

The amount of misreporting of Veterans Administration (VA) benefits was assessed, along with the impact of misreporting on the Basic Educational Opportunity Grant (BEOG) program. Accurate financial information is need to determine appropriate awards. The analysis revealed: over 97% of VA beneficiaries misreported benefits; the total net loss to…

Effects of nonthermal distribution of electrons and polarity of net dust-charge number density on nonplanar dust-ion-acoustic solitary waves.

PubMed

Mamun, A A; Shukla, P K

2009-09-01

Effects of the nonthermal distribution of electrons as well as the polarity of the net dust-charge number density on nonplanar (viz. cylindrical and spherical) dust-ion-acoustic solitary waves (DIASWs) are investigated by employing the reductive perturbation method. It is found that the basic features of the DIASWs are significantly modified by the effects of nonthermal electron distribution, polarity of net dust-charge number density, and nonplanar geometry. The implications of our results in some space and laboratory dusty plasma environments are briefly discussed.

Number of nitrate groups determines reactivity and potency of organic nitrates: a proof of concept study in ALDH-2−/− mice

PubMed Central

Wenzel, P; Hink, U; Oelze, M; Seeling, A; Isse, T; Bruns, K; Steinhoff, L; Brandt, M; Kleschyov, A L; Schulz, E; Lange, K; Weiner, H; Lehmann, J; Lackner, K J; Kawamoto, T; Münzel, T; Daiber, A

2007-01-01

Background and purpose: Mitochondrial aldehyde dehydrogenase (ALDH-2) has been shown to provide a pathway for bioactivation of organic nitrates and to be prone to desensitization in response to highly potent, but not to less potent, nitrates. We therefore sought to support the hypothesis that bioactivation by ALDH-2 critically depends on the number of nitrate groups within the nitrovasodilator. Experimental approach: Nitrates with one (PEMN), two (PEDN; GDN), three (PETriN; glyceryl trinitrate, GTN) and four (pentaerithrityl tetranitrate, PETN) nitrate groups were investigated. Vasodilatory potency was measured in isometric tension studies using isolated aortic segments of wild type (WT) and ALDH-2−/− mice. Activity of the cGMP-dependent kinase-I (reflected by levels of phosphorylated VAsodilator Stimulated Phosphoprotein, P-VASP) was quantified by Western blot analysis, mitochondrial dehydrogenase activity by HPLC. Following incubation of isolated mitochondria with PETN, PETriN-chromophore and PEDN, metabolites were quantified using chemiluminescence nitrogen detection and mass spectrometry. Key results: Compared to WT, vasorelaxation in response to PETN, PETriN and GTN was attenuated about 10fold in ALDH-2−/− mice, identical to WT vessels preincubated with inhibitors of ALDH-2. Reduced vasodilator potency correlated with reduced P-VASP formation and diminished biotransformation of the tetranitrate- and trinitrate-compounds. None of these findings were observed for PEDN, GDN and PEMN. Conclusions and implications: Our results support the crucial role of ALDH-2 in bioactivating highly reactive nitrates like GTN, PETN and PETriN. ALDH-2-mediated relaxation by organic nitrates therefore depends mainly on the number of nitrate groups. Less potent nitrates like PEDN, GDN and PEMN are apparently biotransformed by other pathways. PMID:17220910

Microstamped Petri Dishes for Scanning Electrochemical Microscopy Analysis of Arrays of Microtissues

PubMed Central

Sridhar, Adithya; de Boer, Hans L.; van den Berg, Albert; Le Gac, Séverine

2014-01-01

While scanning electrochemical microscopy (SECM) is a powerful technique for non-invasive analysis of cells, SECM-based assays remain scarce and have been mainly limited so far to single cells, which is mostly due to the absence of suitable platform for experimentation on 3D cellular aggregates or microtissues. Here, we report stamping of a Petri dish with a microwell array for large-scale production of microtissues followed by their in situ analysis using SECM. The platform is realized by hot embossing arrays of microwells (200 μm depth; 400 μm diameter) in commercially available Petri dishes, using a PDMS stamp. Microtissues form spontaneously in the microwells, which is demonstrated here using various cell lines (e.g., HeLa, C2C12, HepG2 and MCF-7). Next, the respiratory activity of live HeLa microtissues is assessed by monitoring the oxygen reduction current in constant height mode and at various distances above the platform surface. Typically, at a 40 μm distance from the microtissue, a 30% decrease in the oxygen reduction current is measured, while above 250 μm, no influence of the presence of the microtissues is detected. After exposure to a model drug (50% ethanol), no such changes in oxygen concentration are found at any height in solution, which reflects that microtissues are not viable anymore. This is furthermore confirmed using conventional live/dead fluorescent stains. This live/dead assay demonstrates the capability of the proposed approach combining SECM and microtissue arrays formed in a stamped Petri dish for conducting cellular assays in a non-invasive way on 3D cellular models. PMID:24690887

An Extensible NetLogo Model for Visualizing Message Routing Protocols

DTIC Science & Technology

2017-08-01

the hard sciences to the social sciences to computer-generated art. NetLogo represents the world as a set of...describe the model is shown here; for the supporting methods , refer to the source code. Approved for public release; distribution is unlimited. 4 iv...if ticks - last-inject > time-to-inject [inject] if run# > #runs [stop] end Next, we present some basic statistics collected for the

A Policy of Individualization and Flexibility Ignoring the Situation of Non-Self-Reliant Individuals: The Example of Swedish Basic Adult Education

ERIC Educational Resources Information Center

Loeb, Ingrid Henning; Wass, Karin Lumsden

2014-01-01

Based on a case study in Swedish municipal basic adult education this article addresses current policies for providing individualized and flexible learning, which have been reinforced in recent adult education reforms. Concepts from the organization theory of "action nets" have been used. Institutionalized procedures and a number of…

Gods, Germs, and Petri Dishes: Toward a Nonsecular Medical Anthropology.

PubMed

Roberts, Elizabeth F S

2016-01-01

This commentary calls on medical anthropology to become programmatically non-secular. Despite recent anthropological critiques of secularity, within and outside of anthropology, most contemporary medical anthropologists continue to leave deities and religiosity out of their examinations of healing practices, especially in their accounts of biomedicine. Through a critical, relational constructionist lens, which traces how all entities are both constructed and real, a non-secular medical anthropology would insist that when deities are part of medical practice, they are integral to analysis. Importantly then, within the symmetrical nature of this same constructionist lens, biomedical entities like germs and petri dishes need to be accounted for just as much as deities.

Antagonism of Trichoderma isolates against Leucoagaricus gongylophorus (Singer) Möller.

PubMed

do Nascimento, Mariela Otoni; de Almeida Sarmento, Renato; Dos Santos, Gil Rodrigues; de Oliveira, Cléia Almeida; de Souza, Danival José

2017-08-01

Filamentous fungi from the genus Trichoderma are commonly found in soil. They are considered facultative mycoparasites, and are antagonists of other fungi such as the cultivar of leaf-cutting ants (Leucoagaricus gongylophorus). The aim of the present study was to bioprospect Trichoderma spp. from different soils collected from Gurupi, Tocantins, Brazil, for antagonistic effects against the mutualistic fungus of leaf-cutting ants. To isolate filamentous fungi, samples were collected from six locations. Preliminarily, isolates were identified by morphological analysis as belonging to Trichoderma. Trichoderma spp. had their internal transcribed spacer region (ITS) of ribosomal RNA genes (rRNA) sequenced to confirm species-level taxonomy. L. gongylophorus was isolated from a laboratory ant colony. Antagonistic properties of seven isolates of Trichoderma against L. gongylophorus were measured using paired disks in Petri dishes with potato dextrose agar medium (PDA). All Trichoderma isolates inhibited the growth of L. gongylophorus in Petri dishes. Isolate 2 of Trichoderma spirale group exhibited slow mycelial growth in the Petri dish, and a high rate of inhibition against L. gongylophorus. This isolate is a promising fungus for field tests of biological control methods for leaf-cutting ants. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Grid-Connected Distributed Generation: Compensation Mechanism Basics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Aznar, Alexandra Y; Zinaman, Owen R

2017-10-02

This short report defines compensation mechanisms for grid-connected, behind-the-meter distributed generation (DG) systems as instruments that comprise three core elements: (1) metering and billing arrangements, (2) sell rate design, and (3) retail rate design. This report describes metering and billing arrangements, with some limited discussion of sell rate design. We detail the three possible arrangements for metering and billing of DG: net energy metering (NEM); buy all, sell all; and net billing.

24 CFR 200.926e - Supplemental information for use with the CABO One and Two Family Dwelling Code.

Code of Federal Regulations, 2014 CFR

2014-04-01

... shall be in accordance with section 7 of ASCE 7-88. (c) Wind pressures. The minimum Design Wind Pressures (net pressures) set forth below apply to areas designated as experiencing basic wind speeds up to and including 80 mph, as shown in ASCE 7-88, Figure 1, Basic Wind Speed Map. These pressures also...

24 CFR 200.926e - Supplemental information for use with the CABO One and Two Family Dwelling Code.

Code of Federal Regulations, 2013 CFR

2013-04-01

... shall be in accordance with section 7 of ASCE 7-88. (c) Wind pressures. The minimum Design Wind Pressures (net pressures) set forth below apply to areas designated as experiencing basic wind speeds up to and including 80 mph, as shown in ASCE 7-88, Figure 1, Basic Wind Speed Map. These pressures also...

24 CFR 200.926e - Supplemental information for use with the CABO One and Two Family Dwelling Code.

Code of Federal Regulations, 2012 CFR

2012-04-01

... shall be in accordance with section 7 of ASCE 7-88. (c) Wind pressures. The minimum Design Wind Pressures (net pressures) set forth below apply to areas designated as experiencing basic wind speeds up to and including 80 mph, as shown in ASCE 7-88, Figure 1, Basic Wind Speed Map. These pressures also...

24 CFR 200.926e - Supplemental information for use with the CABO One and Two Family Dwelling Code.

Code of Federal Regulations, 2010 CFR

2010-04-01

... shall be in accordance with section 7 of ASCE 7-88. (c) Wind pressures. The minimum Design Wind Pressures (net pressures) set forth below apply to areas designated as experiencing basic wind speeds up to and including 80 mph, as shown in ASCE 7-88, Figure 1, Basic Wind Speed Map. These pressures also...

24 CFR 200.926e - Supplemental information for use with the CABO One and Two Family Dwelling Code.

Code of Federal Regulations, 2011 CFR

2011-04-01

... shall be in accordance with section 7 of ASCE 7-88. (c) Wind pressures. The minimum Design Wind Pressures (net pressures) set forth below apply to areas designated as experiencing basic wind speeds up to and including 80 mph, as shown in ASCE 7-88, Figure 1, Basic Wind Speed Map. These pressures also...

Understanding your cancer prognosis

MedlinePlus

... about: Treatment Palliative care Personal matters such as finances Knowing what to expect may make it easier ... treatment. www.cancer.net/navigating-cancer-care/cancer-basics/understanding-statistics-used-guide-prognosis-and-evaluate-treatment . ...

Formal Verification of Safety Properties for Aerospace Systems Through Algorithms Based on Exhaustive State-Space Exploration

NASA Technical Reports Server (NTRS)

Ciardo, Gianfranco

2004-01-01

The Runway Safety Monitor (RSM) designed by Lockheed Martin is part of NASA's effort to reduce aviation accidents. We developed a Petri net model of the RSM protocol and used the model checking functions of our tool SMART to investigate a number of safety properties in RSM. To mitigate the impact of state-space explosion, we built a highly discretized model of the system, obtained by partitioning the monitored runway zone into a grid of smaller volumes and by considering scenarios involving only two aircraft. The model also assumes that there are no communication failures, such as bad input from radar or lack of incoming data, thus it relies on a consistent view of reality by all participants. In spite of these simplifications, we were able to expose potential problems in the RSM conceptual design. Our findings were forwarded to the design engineers, who undertook corrective action. Additionally, the results stress the efficiency attained by the new model checking algorithms implemented in SMART, and demonstrate their applicability to real-world systems. Attempts to verify RSM with NuSMV and SPIN have failed due to excessive memory consumption.

A web-based rapid assessment tool for production publishing solutions

NASA Astrophysics Data System (ADS)

Sun, Tong

2010-02-01

Solution assessment is a critical first-step in understanding and measuring the business process efficiency enabled by an integrated solution package. However, assessing the effectiveness of any solution is usually a very expensive and timeconsuming task which involves lots of domain knowledge, collecting and understanding the specific customer operational context, defining validation scenarios and estimating the expected performance and operational cost. This paper presents an intelligent web-based tool that can rapidly assess any given solution package for production publishing workflows via a simulation engine and create a report for various estimated performance metrics (e.g. throughput, turnaround time, resource utilization) and operational cost. By integrating the digital publishing workflow ontology and an activity based costing model with a Petri-net based workflow simulation engine, this web-based tool allows users to quickly evaluate any potential digital publishing solutions side-by-side within their desired operational contexts, and provides a low-cost and rapid assessment for organizations before committing any purchase. This tool also benefits the solution providers to shorten the sales cycles, establishing a trustworthy customer relationship and supplement the professional assessment services with a proven quantitative simulation and estimation technology.

The Systems Biology Markup Language (SBML) Level 3 Package: Qualitative Models, Version 1, Release 1.

PubMed

Chaouiya, Claudine; Keating, Sarah M; Berenguier, Duncan; Naldi, Aurélien; Thieffry, Denis; van Iersel, Martijn P; Le Novère, Nicolas; Helikar, Tomáš

2015-09-04

Quantitative methods for modelling biological networks require an in-depth knowledge of the biochemical reactions and their stoichiometric and kinetic parameters. In many practical cases, this knowledge is missing. This has led to the development of several qualitative modelling methods using information such as, for example, gene expression data coming from functional genomic experiments. The SBML Level 3 Version 1 Core specification does not provide a mechanism for explicitly encoding qualitative models, but it does provide a mechanism for SBML packages to extend the Core specification and add additional syntactical constructs. The SBML Qualitative Models package for SBML Level 3 adds features so that qualitative models can be directly and explicitly encoded. The approach taken in this package is essentially based on the definition of regulatory or influence graphs. The SBML Qualitative Models package defines the structure and syntax necessary to describe qualitative models that associate discrete levels of activities with entity pools and the transitions between states that describe the processes involved. This is particularly suited to logical models (Boolean or multi-valued) and some classes of Petri net models can be encoded with the approach.

Two-layer symbolic representation for stochastic models with phase-type distributed events

NASA Astrophysics Data System (ADS)

Longo, Francesco; Scarpa, Marco

2015-07-01

Among the techniques that have been proposed for the analysis of non-Markovian models, the state space expansion approach showed great flexibility in terms of modelling capacities.The principal drawback is the explosion of the state space. This paper proposes a two-layer symbolic method for efficiently storing the expanded reachability graph of a non-Markovian model in the case in which continuous phase-type distributions are associated with the firing times of system events, and different memory policies are considered. At the lower layer, the reachability graph is symbolically represented in the form of a set of Kronecker matrices, while, at the higher layer, all the information needed to correctly manage event memory is stored in a multi-terminal multi-valued decision diagram. Such an information is collected by applying a symbolic algorithm, which is based on a couple of theorems. The efficiency of the proposed approach, in terms of memory occupation and execution time, is shown by applying it to a set of non-Markovian stochastic Petri nets and comparing it with a classical explicit expansion algorithm. Moreover, a comparison with a classical symbolic approach is performed whenever possible.

Healthcare information technology infrastructures in Turkey.

PubMed

Dogac, A; Yuksel, M; Ertürkmen, G L; Kabak, Y; Namli, T; Yıldız, M H; Ay, Y; Ceyhan, B; Hülür, U; Oztürk, H; Atbakan, E

2014-05-22

The objective of this paper is to describe some of the major healthcare information technology (IT) infrastructures in Turkey, namely, Sağlık-Net (Turkish for "Health-Net"), the Centralized Hospital Appointment System, the Basic Health Statistics Module, the Core Resources Management System, and the e-prescription system of the Social Security Institution. International collaboration projects that are integrated with Sağlık-Net are also briefly summarized. The authors provide a survey of the some of the major healthcare IT infrastructures in Turkey. Sağlık-Net has two main components: the National Health Information System (NHIS) and the Family Medicine Information System (FMIS). The NHIS is a nation-wide infrastructure for sharing patients' Electronic Health Records (EHRs). So far, EHRs of 78.9 million people have been created in the NHIS. Similarly, family medicine is operational in the whole country via FMIS. Centralized Hospital Appointment System enables the citizens to easily make appointments in healthcare providers. Basic Health Statistics Module is used for collecting information about the health status, risks and indicators across the country. Core Resources Management System speeds up the flow of information between the headquarters and Provincial Health Directorates. The e-prescription system is linked with Sağlık-Net and seamlessly integrated with the healthcare provider information systems. Finally, Turkey is involved in several international projects for experience sharing and disseminating national developments. With the introduction of the "Health Transformation Program" in 2003, a number of successful healthcare IT infrastructures have been developed in Turkey. Currently, work is going on to enhance and further improve their functionality.

Apparatus and process for microbial detection and enumeration

NASA Technical Reports Server (NTRS)

Wilkins, J. R.; Grana, D. (Inventor)

1982-01-01

An apparatus and process for detecting and enumerating specific microorganisms from large volume samples containing small numbers of the microorganisms is presented. The large volume samples are filtered through a membrane filter to concentrate the microorganisms. The filter is positioned between two absorbent pads and previously moistened with a growth medium for the microorganisms. A pair of electrodes are disposed against the filter and the pad electrode filter assembly is retained within a petri dish by retainer ring. The cover is positioned on base of petri dish and sealed at the edges by a parafilm seal prior to being electrically connected via connectors to a strip chart recorder for detecting and enumerating the microorganisms collected on filter.

Pt-coated cylindrical micropatterned honeycomb Petri dishes as an efficient TCO-free counter electrode in liquid junction photovoltaic devices

NASA Astrophysics Data System (ADS)

Dao, Van-Duong; Bui, Van-Tien; Choi, Ho-Suk

2018-02-01

The Pt layer deposited on a cylindrical micro cavity patterned Petri dish, which is produced using a one-step solvent-immersion phase separation, is fabricated for the first time as an FTO-free counter electrode (CE) for dye-sensitized solar cells (DSCs). Due to the high specific active surface area of the Pt-deposited honeycomb substrate CE, the efficiency of the DSC using the developed CE substrate is enhanced by 14.5% compared with the device using a Pt-sputtered flat substrate. This design strategy has potential in fabricating highly efficient and low-cost CE materials with FTO-free substrates for DSCs.

Measurement of net electric charge and dipole moment of dust aggregates in a complex plasma.

PubMed

Yousefi, Razieh; Davis, Allen B; Carmona-Reyes, Jorge; Matthews, Lorin S; Hyde, Truell W

2014-09-01

Understanding the agglomeration of dust particles in complex plasmas requires knowledge of basic properties such as the net electrostatic charge and dipole moment of the dust. In this study, dust aggregates are formed from gold-coated mono-disperse spherical melamine-formaldehyde monomers in a radiofrequency (rf) argon discharge plasma. The behavior of observed dust aggregates is analyzed both by studying the particle trajectories and by employing computer models examining three-dimensional structures of aggregates and their interactions and rotations as induced by torques arising from their dipole moments. These allow the basic characteristics of the dust aggregates, such as the electrostatic charge and dipole moment, as well as the external electric field, to be determined. It is shown that the experimental results support the predicted values from computer models for aggregates in these environments.

Basic research and data analysis for the National Geodetic Satellite program and for the Earth Surveys program

NASA Technical Reports Server (NTRS)

1972-01-01

Current research is reported on precise and accurate descriptions of the earth's surface and gravitational field and on time variations of geophysical parameters. A new computer program was written in connection with the adjustment of the BC-4 worldwide geometric satellite triangulation net. The possibility that an increment to accuracy could be transferred from a super-control net to the basic geodetic (first-order triangulation) was investigated. Coordinates of the NA9 solution were computed and were transformed to the NAD datum, based on GEOS 1 observations. Normal equations from observational data of several different systems and constraint equations were added and a single solution was obtained for the combined systems. Transformation parameters with constraints were determined, and the impact of computers on surveying and mapping is discussed.

A climate-based malaria model with the use of bed nets.

PubMed

Wang, Xiunan; Zhao, Xiao-Qiang

2018-07-01

Insecticide-treated bed nets (ITNs) are among the most important and effective intervention measures against malaria. In order to investigate the impact of bed net use on disease control, we formulate a periodic vector-bias malaria model incorporating the juvenile stage of mosquitoes and the use of ITNs. We derive the vector reproduction ratio [Formula: see text] and the basic reproduction ratio [Formula: see text]. We show that the global dynamics of the model is completely determined by these two reproduction ratios. More precisely, the mosquito-free periodic solution is globally attractive if [Formula: see text]; the unique disease-free periodic solution is globally attractive if [Formula: see text] and [Formula: see text]; and the model admits a unique positive periodic solution and it is globally attractive if [Formula: see text] and [Formula: see text]. Numerically, we study the malaria transmission case in Port Harcourt, Nigeria. Our findings show that the use of ITNs has a positive effect on reducing [Formula: see text], and that malaria may be eliminated from this area if over 75% of the human population were to use ITNs. The simulation about the long term behavior of solutions has good agreement with the obtained analytic result. Moreover, we find that the ignorance of the vector-bias effect may result in underestimation of the basic reproduction ratio [Formula: see text]. Another notable result is that the infection risk would be underestimated if the basic reproduction ratio [Formula: see text] of the time-averaged autonomous system were used.

Selective sweeps in growing microbial colonies

NASA Astrophysics Data System (ADS)

Korolev, Kirill S.; Müller, Melanie J. I.; Karahan, Nilay; Murray, Andrew W.; Hallatschek, Oskar; Nelson, David R.

2012-04-01

Evolutionary experiments with microbes are a powerful tool to study mutations and natural selection. These experiments, however, are often limited to the well-mixed environments of a test tube or a chemostat. Since spatial organization can significantly affect evolutionary dynamics, the need is growing for evolutionary experiments in spatially structured environments. The surface of a Petri dish provides such an environment, but a more detailed understanding of microbial growth on Petri dishes is necessary to interpret such experiments. We formulate a simple deterministic reaction-diffusion model, which successfully predicts the spatial patterns created by two competing species during colony expansion. We also derive the shape of these patterns analytically without relying on microscopic details of the model. In particular, we find that the relative fitness of two microbial strains can be estimated from the logarithmic spirals created by selective sweeps. The theory is tested with strains of the budding yeast Saccharomyces cerevisiae for spatial competitions with different initial conditions and for a range of relative fitnesses. The reaction-diffusion model also connects the microscopic parameters like growth rates and diffusion constants with macroscopic spatial patterns and predicts the relationship between fitness in liquid cultures and on Petri dishes, which we confirmed experimentally. Spatial sector patterns therefore provide an alternative fitness assay to the commonly used liquid culture fitness assays.

Pancreatic neuroendocrine tumors: the basics, the gray zone, and the target.

PubMed

Kelgiorgi, Dionysia; Dervenis, Christos

2017-01-01

Pancreatic neuroendocrine tumors (PanNETs) manifest with a range of symptoms and pose a therapeutic challenge. A team approach, in which many specialists come together, is necessary in the quest for the best patient-tailored treatment. Disciplines such as oncology, surgery, basic science, endocrinology, radiology, and nuclear medicine need to work side by side, equally contributing to patient care and to advancing our better understanding of this fascinating disease.

Ethylene induced shikonin biosynthesis in shoot culture of Lithospermum erythrorhizon.

PubMed

Touno, Kaori; Tamaoka, Jin; Ohashi, Yuko; Shimomura, Koichiro

2005-02-01

Lithospermum erythrorhizon shoots, cultured on phytohormone-free Murashige and Skoog solid medium, produced shikonin derivatives, whereas shoots cultured in well-ventilated petri dishes, produced small amount. Analysis by gas chromatography revealed the presence of ethylene in non-ventilated petri dishes where the shoots, producing shikonin derivatives, were cultured. Therefore, the possible involvement of ethylene in shikonin biosynthesis of shoot cultures was investigated. Treatment of ethylene or the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, resulted in increasing shikonin derivatives contents in cultured shoots. Silver ion, an ethylene-response inhibitor, or aminoethoxyvinylglycine, an ethylene biosynthesis inhibitor, decreased production of shikonin derivatives in cultured shoots. Our results indicate that ethylene is one of the regulatory elements of shikonin biosynthesis in L. erythrorhizon shoot culture.

Machine for Automatic Bacteriological Pour Plate Preparation

PubMed Central

Sharpe, A. N.; Biggs, D. R.; Oliver, R. J.

1972-01-01

A fully automatic system for preparing poured plates for bacteriological analyses has been constructed and tested. The machine can make decimal dilutions of bacterial suspensions, dispense measured amounts into petri dishes, add molten agar, mix the dish contents, and label the dishes with sample and dilution numbers at the rate of 2,000 dishes per 8-hr day. In addition, the machine can be programmed to select different media so that plates for different types of bacteriological analysis may be made automatically from the same sample. The machine uses only the components of the media and sterile polystyrene petri dishes; requirements for all other materials, such as sterile pipettes and capped bottles of diluents and agar, are eliminated. Images PMID:4560475

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. The petri plates are wrapped in black cloth and kept cold (+4 degrees Celsius) to prevent them from germinating prior to the experiment start on station. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Uptake of free amino acids by bacteria-free larvae of the sand dollar Dendraster excentricus.

PubMed

Davis, J P; Stephens, G C

1984-10-01

Larvae of Dendraster excentricus were produced by collecting gametes and carrying out fertilization under aseptic conditions. Since gametes are free of bacteria in the gonad, bacteria-free (axenic) suspensions of larvae result. Net rates of entry of 14 amino acids and the rate of production of ammonia were simultaneously determined by high-performance liquid chromatography. The net rates of uptake of neutral amino acids were an order of magnitude greater than rates for basic and acidic amino acids. Influx of 14C-labeled leucine, arginine, and glutamate accurately reflects the net entry rate of these substrates. Uptake of amino acids by axenic suspensions of larvae was compared with uptake by suspensions prepared without aseptic precautions. There was no significant difference in net uptake of the 14 amino acids or in the pattern of oxidation and assimilation of [14C]leucine during short-term experiments of 4-h duration or less.

A Study of NetCDF as an Approach for High Performance Medical Image Storage

NASA Astrophysics Data System (ADS)

Magnus, Marcone; Coelho Prado, Thiago; von Wangenhein, Aldo; de Macedo, Douglas D. J.; Dantas, M. A. R.

2012-02-01

The spread of telemedicine systems increases every day. The systems and PACS based on DICOM images has become common. This rise reflects the need to develop new storage systems, more efficient and with lower computational costs. With this in mind, this article discusses a study for application in NetCDF data format as the basic platform for storage of DICOM images. The study case comparison adopts an ordinary database, the HDF5 and the NetCDF to storage the medical images. Empirical results, using a real set of images, indicate that the time to retrieve images from the NetCDF for large scale images has a higher latency compared to the other two methods. In addition, the latency is proportional to the file size, which represents a drawback to a telemedicine system that is characterized by a large amount of large image files.

MediaNet: a multimedia information network for knowledge representation

NASA Astrophysics Data System (ADS)

Benitez, Ana B.; Smith, John R.; Chang, Shih-Fu

2000-10-01

In this paper, we present MediaNet, which is a knowledge representation framework that uses multimedia content for representing semantic and perceptual information. The main components of MediaNet include conceptual entities, which correspond to real world objects, and relationships among concepts. MediaNet allows the concepts and relationships to be defined or exemplified by multimedia content such as images, video, audio, graphics, and text. MediaNet models the traditional relationship types such as generalization and aggregation but adds additional functionality by modeling perceptual relationships based on feature similarity. For example, MediaNet allows a concept such as car to be defined as a type of a transportation vehicle, but which is further defined and illustrated through example images, videos and sounds of cars. In constructing the MediaNet framework, we have built on the basic principles of semiotics and semantic networks in addition to utilizing the audio-visual content description framework being developed as part of the MPEG-7 multimedia content description standard. By integrating both conceptual and perceptual representations of knowledge, MediaNet has potential to impact a broad range of applications that deal with multimedia content at the semantic and perceptual levels. In particular, we have found that MediaNet can improve the performance of multimedia retrieval applications by using query expansion, refinement and translation across multiple content modalities. In this paper, we report on experiments that use MediaNet in searching for images. We construct the MediaNet knowledge base using both WordNet and an image network built from multiple example images and extracted color and texture descriptors. Initial experimental results demonstrate improved retrieval effectiveness using MediaNet in a content-based retrieval system.

Natural Selection in a Petri Dish.

ERIC Educational Resources Information Center

McCarty, Robbie V.; Marek, Edmund A.

1997-01-01

Presents an activity to teach natural selection that involves students in a microbiological investigation. Students discover that a change in environmental conditions tests a species' range of adaptations. (DDR)

Antimicrobial Testing Methods & Procedures: MB-33-00

EPA Pesticide Factsheets

Information about ATMP - SOP Quantitative Petri Plate Method (QPM) for Determining the Effectiveness of Antimicrobial Towelettes Against Vegetative Bacteria on Inanimate, Hard, Non-porous Surfaces - MB-33-00

RIPGIS-NET: a GIS tool for riparian groundwater evapotranspiration in MODFLOW.

PubMed

Ajami, Hoori; Maddock, Thomas; Meixner, Thomas; Hogan, James F; Guertin, D Phillip

2012-01-01

RIPGIS-NET, an Environmental System Research Institute (ESRI's) ArcGIS 9.2/9.3 custom application, was developed to derive parameters and visualize results of spatially explicit riparian groundwater evapotranspiration (ETg), evapotranspiration from saturated zone, in groundwater flow models for ecohydrology, riparian ecosystem management, and stream restoration. Specifically RIPGIS-NET works with riparian evapotranspiration (RIP-ET), a modeling package that works with the MODFLOW groundwater flow model. RIP-ET improves ETg simulations by using a set of eco-physiologically based ETg curves for plant functional subgroups (PFSGs), and separates ground evaporation and plant transpiration processes from the water table. The RIPGIS-NET program was developed in Visual Basic 2005, .NET framework 2.0, and runs in ArcMap 9.2 and 9.3 applications. RIPGIS-NET, a pre- and post-processor for RIP-ET, incorporates spatial variability of riparian vegetation and land surface elevation into ETg estimation in MODFLOW groundwater models. RIPGIS-NET derives RIP-ET input parameters including PFSG evapotranspiration curve parameters, fractional coverage areas of each PFSG in a MODFLOW cell, and average surface elevation per riparian vegetation polygon using a digital elevation model. RIPGIS-NET also provides visualization tools for modelers to create head maps, depth to water table (DTWT) maps, and plot DTWT for a PFSG in a polygon in the Geographic Information System based on MODFLOW simulation results. © 2011, The Author(s). Ground Water © 2011, National Ground Water Association.

Peptidylarginine deiminase 4: a nuclear button triggering neutrophil extracellular traps in inflammatory diseases and aging.

PubMed

Wong, Siu Ling; Wagner, Denisa D

2018-06-20

Peptidylarginine deiminase 4 (PAD4) is a nuclear citrullinating enzyme that is critically involved in the release of decondensed chromatin from neutrophils as neutrophil extracellular traps (NETs). NETs, together with fibrin, are implicated in host defense against pathogens; however, the formation of NETs (NETosis) has injurious effects that may outweigh their protective role. For example, PAD4 activity produces citrullinated neoantigens that promote autoimmune diseases, such as rheumatoid arthritis, to which PAD4 is genetically linked and where NETosis is prominent. NETs are also generated in basic sterile inflammatory responses that are induced by many inflammatory stimuli, including cytokines, hypoxia, and activated platelets. Mice that lack PAD4-deficient in NETosis-serve as an excellent tool with which to study the importance of NETs in disease models. In recent years, animal and human studies have demonstrated that NETs contribute to the etiology and propagation of many common noninfectious diseases, the focus of our review. We will discuss the role of NETs in thrombotic and cardiovascular disease, the induction of NETs by cancers and its implications for cancer progression and cancer-associated thrombosis, and elevated NETosis in diabetes and its negative impact on wound healing, and will propose a link between PAD4/NETs and age-related organ fibrosis. We identify unresolved issues and new research directions.-Wong, S. L., Wagner, D. D. Peptidylarginine deiminase 4: a nuclear button triggering neutrophil extracellular traps in inflammatory diseases and aging.

Hollow-Fiber Membrane Chamber as a Device for In Situ Environmental Cultivation▿

PubMed Central

Aoi, Yoshiteru; Kinoshita, Tomoyuki; Hata, Toru; Ohta, Hiroaki; Obokata, Haruko; Tsuneda, Satoshi

2009-01-01

A hollow-fiber membrane chamber (HFMC) was developed as an in situ cultivation device for environmental microorganisms. The HFMC system consists of 48 to 96 pieces of porous hollow-fiber membrane connected with injectors. The system allows rapid exchange of chemical compounds, thereby simulating a natural environment. Comparative analysis through the cultivation of three types of environmental samples was performed using this newly designed device and a conventional agar-based petri dish. The results show that the ratios of novel phylotypes in isolates, species-level diversities, and cultivabilities in HFMC-based cultivation are higher than those in an agar-based petri dish for all three samples, suggesting that the new in situ cultivation device is effective for cultivation of various environmental microorganisms. PMID:19329655

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. Eric Morris from the cold stowage group fits items into the Double Cold Bag (DCB) which is a non-powered container that keeps the APEX petri plates at +4 degrees Celsius during launch and ascent.. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. The 30 petri plates are bundled into groups of 10 and placed into one of three science kits. The science kits allow easy handling when the crew removes the plates from cold stowage on station. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

An 802.11 n wireless local area network transmission scheme for wireless telemedicine applications.

PubMed

Lin, C F; Hung, S I; Chiang, I H

2010-10-01

In this paper, an 802.11 n transmission scheme is proposed for wireless telemedicine applications. IEEE 802.11n standards, a power assignment strategy, space-time block coding (STBC), and an object composition Petri net (OCPN) model are adopted. With the proposed wireless system, G.729 audio bit streams, Joint Photographic Experts Group 2000 (JPEG 2000) clinical images, and Moving Picture Experts Group 4 (MPEG-4) video bit streams achieve a transmission bit error rate (BER) of 10-7, 10-4, and 103 simultaneously. The proposed system meets the requirements prescribed for wireless telemedicine applications. An essential feature of this proposed transmission scheme is that clinical information that requires a high quality of service (QoS) is transmitted at a high power transmission rate with significant error protection. For maximizing resource utilization and minimizing the total transmission power, STBC and adaptive modulation techniques are used in the proposed 802.11 n wireless telemedicine system. Further, low power, direct mapping (DM), low-error protection scheme, and high-level modulation are adopted for messages that can tolerate a high BER. With the proposed transmission scheme, the required reliability of communication can be achieved. Our simulation results have shown that the proposed 802.11 n transmission scheme can be used for developing effective wireless telemedicine systems.

Using Business Process Specification and Agent to Integrate a Scenario Driven Supply Chain

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cho, Hyunbo; Kulvatunyou, Boonserm; Jeong, Hanil

2004-07-01

In today's increasingly competitive global market, most enterprises place high priority on reducing order-fulfillment costs, minimizing time-to-market, and maximizing product quality. The desire of businesses to achieve these goals has seen a shift from a make-to-stock paradigm to a make-to-order paradigm. The success of this new paradigm requires robust and efficient supply chain integration and the ability to operate in the business-to-business (B2B) environment. Recent internet-based approaches have enabled instantaneous and secure information sharing among trading partners (i.e., customers, manufacturers, and suppliers). In this paper, we present a framework that enables both integration and B2B operations. This framework uses pre-definedmore » business process specifications (BPS) and agent technologies. The BPS, which specifies a message choreography among the trading partners, is modeled using a modified Unified Modeling Language (UML). The behavior of the enterprise applications within each trading partner -- how they respond to external events specified in the BPS -- is modeled using Petri-nets and implemented as a collection of agents. The concepts and models proposed in this paper should provide the starting point for the formulation of a structured approach to B2B supply chain integration and implementation.« less

Reliable Execution Based on CPN and Skyline Optimization for Web Service Composition

PubMed Central

Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets. PMID:23935431

Resource utilization model for the algorithm to architecture mapping model

NASA Technical Reports Server (NTRS)

Stoughton, John W.; Patel, Rakesh R.

1993-01-01

The analytical model for resource utilization and the variable node time and conditional node model for the enhanced ATAMM model for a real-time data flow architecture are presented in this research. The Algorithm To Architecture Mapping Model, ATAMM, is a Petri net based graph theoretic model developed at Old Dominion University, and is capable of modeling the execution of large-grained algorithms on a real-time data flow architecture. Using the resource utilization model, the resource envelope may be obtained directly from a given graph and, consequently, the maximum number of required resources may be evaluated. The node timing diagram for one iteration period may be obtained using the analytical resource envelope. The variable node time model, which describes the change in resource requirement for the execution of an algorithm under node time variation, is useful to expand the applicability of the ATAMM model to heterogeneous architectures. The model also describes a method of detecting the presence of resource limited mode and its subsequent prevention. Graphs with conditional nodes are shown to be reduced to equivalent graphs with time varying nodes and, subsequently, may be analyzed using the variable node time model to determine resource requirements. Case studies are performed on three graphs for the illustration of applicability of the analytical theories.

Anonymity-preserving Reputation Management System for health sector

PubMed Central

Hamid, Zara; Abdul, Wadood; Ghouzali, Sanaa; Khan, Abid; Malik, Saif Ur Rehman; Shaukat Khan, Mansoor; Nawaz, Sarfraz

2018-01-01

In health sector, trust is considered important because it indirectly influences the quality of health care through patient satisfaction, adherence and the continuity of its relationship with health care professionals and the promotion of accurate and timely diagnoses. One of the important requirements of TRSs in the health sector is rating secrecy, which mandates that the identification information about the service consumer should be kept secret to prevent any privacy violation. Anonymity and trust are two imperative objectives, and no significant explicit efforts have been made to achieve both of them at the same time. In this paper, we present a framework for solving the problem of reconciling trust with anonymity in the health sector. Our solution comprises Anonymous Reputation Management (ARM) protocol and Context-aware Trustworthiness Assessment (CTA) protocol. ARM protocol ensures that only those service consumers who received a service from a specific service provider provide a recommendation score anonymously with in the specified time limit. The CTA protocol computes the reputation of a user as a service provider and as a recommender. To determine the correctness of the proposed ARM protocol, formal modelling and verification are performed using High Level Petri Nets (HLPN) and Z3 Solver. Our simulation results verify the accuracy of the proposed context-aware trust assessment scheme. PMID:29649267

From chart tracking to workflow management.

PubMed Central

Srinivasan, P.; Vignes, G.; Venable, C.; Hazelwood, A.; Cade, T.

1994-01-01

The current interest in system-wide integration appears to be based on the assumption that an organization, by digitizing information and accepting a common standard for the exchange of such information, will improve the accessibility of this information and automatically experience benefits resulting from its more productive use. We do not dispute this reasoning, but assert that an organization's capacity for effective change is proportional to the understanding of the current structure among its personnel. Our workflow manager is based on the use of a Parameterized Petri Net (PPN) model which can be configured to represent an arbitrarily detailed picture of an organization. The PPN model can be animated to observe the model organization in action, and the results of the animation analyzed. This simulation is a dynamic ongoing process which changes with the system and allows members of the organization to pose "what if" questions as a means of exploring opportunities for change. We present, the "workflow management system" as the natural successor to the tracking program, incorporating modeling, scheduling, reactive planning, performance evaluation, and simulation. This workflow management system is more than adequate for meeting the needs of a paper chart tracking system, and, as the patient record is computerized, will serve as a planning and evaluation tool in converting the paper-based health information system into a computer-based system. PMID:7950051

Modeling of the Human - Operator in a Complex System Functioning Under Extreme Conditions

NASA Astrophysics Data System (ADS)

Getzov, Peter; Hubenova, Zoia; Yordanov, Dimitar; Popov, Wiliam

2013-12-01

Problems, related to the explication of sophisticated control systems of objects, operating under extreme conditions, have been examined and the impact of the effectiveness of the operator's activity on the systems as a whole. The necessity of creation of complex simulation models, reflecting operator's activity, is discussed. Organizational and technical system of an unmanned aviation complex is described as a sophisticated ergatic system. Computer realization of main subsystems of algorithmic system of the man as a controlling system is implemented and specialized software for data processing and analysis is developed. An original computer model of a Man as a tracking system has been implemented. Model of unmanned complex for operators training and formation of a mental model in emergency situation, implemented in "matlab-simulink" environment, has been synthesized. As a unit of the control loop, the pilot (operator) is simplified viewed as an autocontrol system consisting of three main interconnected subsystems: sensitive organs (perception sensors); central nervous system; executive organs (muscles of the arms, legs, back). Theoretical-data model of prediction the level of operator's information load in ergatic systems is proposed. It allows the assessment and prediction of the effectiveness of a real working operator. Simulation model of operator's activity in takeoff based on the Petri nets has been synthesized.

Reliable execution based on CPN and skyline optimization for Web service composition.

PubMed

Chen, Liping; Ha, Weitao; Zhang, Guojun

2013-01-01

With development of SOA, the complex problem can be solved by combining available individual services and ordering them to best suit user's requirements. Web services composition is widely used in business environment. With the features of inherent autonomy and heterogeneity for component web services, it is difficult to predict the behavior of the overall composite service. Therefore, transactional properties and nonfunctional quality of service (QoS) properties are crucial for selecting the web services to take part in the composition. Transactional properties ensure reliability of composite Web service, and QoS properties can identify the best candidate web services from a set of functionally equivalent services. In this paper we define a Colored Petri Net (CPN) model which involves transactional properties of web services in the composition process. To ensure reliable and correct execution, unfolding processes of the CPN are followed. The execution of transactional composition Web service (TCWS) is formalized by CPN properties. To identify the best services of QoS properties from candidate service sets formed in the TCSW-CPN, we use skyline computation to retrieve dominant Web service. It can overcome that the reduction of individual scores to an overall similarity leads to significant information loss. We evaluate our approach experimentally using both real and synthetically generated datasets.

Rapid fibroblast activation in mammalian cells induced by silicon nanowire arrays

NASA Astrophysics Data System (ADS)

Ha, Qing; Yang, Gao; Ao, Zhuo; Han, Dong; Niu, Fenglan; Wang, Shutao

2014-06-01

Activated tumor-associated fibroblasts (TAFs) with abundant fibroblast activation protein (FAP) expression attract tremendous attention in tumor progression studies. In this work, we report a rapid 24 h FAP activation method for fibroblasts using silicon nanowires (SiNWs) as culture substrates instead of growth factors or chemokines. In contrast with cells cultured on flat silicon which rarely express FAP, SiNW cultivated cells exhibit FAP levels similar to those found in cancerous tissue. We demonstrated that activated cells grown on SiNWs maintain their viability and proliferation in a time-dependent manner. Moreover, environmental scanning electron microscopy (ESEM) and focused ion beam and scanning electron microscopy (FIB-SEM) analysis clearly revealed that activated cells on SiNWs adapt to the structure of their substrates by filling inter-wire cavities via filopodia in contrast to cells cultured on flat silicon which spread freely. We further illustrated that the expression of FAP was rarely detected in activated cells after being re-cultured in Petri dishes, suggesting that the unique structure of SiNWs may have a certain influence on FAP activation.Activated tumor-associated fibroblasts (TAFs) with abundant fibroblast activation protein (FAP) expression attract tremendous attention in tumor progression studies. In this work, we report a rapid 24 h FAP activation method for fibroblasts using silicon nanowires (SiNWs) as culture substrates instead of growth factors or chemokines. In contrast with cells cultured on flat silicon which rarely express FAP, SiNW cultivated cells exhibit FAP levels similar to those found in cancerous tissue. We demonstrated that activated cells grown on SiNWs maintain their viability and proliferation in a time-dependent manner. Moreover, environmental scanning electron microscopy (ESEM) and focused ion beam and scanning electron microscopy (FIB-SEM) analysis clearly revealed that activated cells on SiNWs adapt to the structure of their substrates by filling inter-wire cavities via filopodia in contrast to cells cultured on flat silicon which spread freely. We further illustrated that the expression of FAP was rarely detected in activated cells after being re-cultured in Petri dishes, suggesting that the unique structure of SiNWs may have a certain influence on FAP activation. Electronic supplementary information (ESI) available: (1) ESEM cross-sectional view images of the flat silicon and SiNW substrates. (2) Bright field morphology images of fibroblasts cultured in Petri dishes. (3) FIB/SEM 52° tilt images of fibroblasts cultured on SiNW 2 and SiNW 3. (4) Immunofluorescence images of FAP expression in fibroblasts re-cultured in Petri dishes after detachment from flat silicon and a series of SiNW substrates. (5) ESEM images of cells re-cultured in Petri dishes after detachment from each group. See DOI: 10.1039/c4nr01415d

New Directions for Corporate Careers.

ERIC Educational Resources Information Center

Lemke, James M.; And Others

1995-01-01

Includes "Introduction" (Lemke); "Career Sidestepping" (Prescott); "Temporary Work Life" (Farrugia); "Electronic Recruiter" (Lemke); "Aerospace Network" (Hoffner); "Multimedia: The Future of Adult Learning" (Golub); and "Teleworking: Commuting on the Information Highway" (Petrie). (JOW)

Selection of Norway spruce somatic embryos by computer vision

NASA Astrophysics Data System (ADS)

Hamalainen, Jari J.; Jokinen, Kari J.

1993-05-01

A computer vision system was developed for the classification of plant somatic embryos. The embryos are in a Petri dish that is transferred with constant speed and they are recognized as they pass a line scan camera. A classification algorithm needs to be installed for every plant species. This paper describes an algorithm for the recognition of Norway spruce (Picea abies) embryos. A short review of conifer micropropagation by somatic embryogenesis is also given. The recognition algorithm is based on features calculated from the boundary of the object. Only part of the boundary corresponding to the developing cotyledons (2 - 15) and the straight sides of the embryo are used for recognition. An index of the length of the cotyledons describes the developmental stage of the embryo. The testing set for classifier performance consisted of 118 embryos and 478 nonembryos. With the classification tolerances chosen 69% of the objects classified as embryos by a human classifier were selected and 31$% rejected. Less than 1% of the nonembryos were classified as embryos. The basic features developed can probably be easily adapted for the recognition of other conifer somatic embryos.

Software Re-Engineering of the Human Factors Analysis and Classification System - (Maintenance Extension) Using Object Oriented Methods in a Microsoft Environment

DTIC Science & Technology

2001-09-01

replication) -- all from Visual Basic and VBA . In fact, we found that the SQL Server engine actually had a plethora of options, most formidable of...2002, the new SQL Server 2000 database engine, and Microsoft Visual Basic.NET. This thesis describes our use of the Spiral Development Model to...versions of Microsoft products? Specifically, the pending release of Microsoft Office 2002, the new SQL Server 2000 database engine, and Microsoft

Static Verification for Code Contracts

NASA Astrophysics Data System (ADS)

Fähndrich, Manuel

The Code Contracts project [3] at Microsoft Research enables programmers on the .NET platform to author specifications in existing languages such as C# and VisualBasic. To take advantage of these specifications, we provide tools for documentation generation, runtime contract checking, and static contract verification.

Using Expected Value to Introduce the Laplace Transform

ERIC Educational Resources Information Center

Lutzer, Carl V.

2015-01-01

We propose an introduction to the Laplace transform in which Riemann sums are used to approximate the expected net change in a function, assuming that it quantifies a process that can terminate at random. We assume only a basic understanding of probability.

GASB 35: The New Financial Reporting Requirements for Public College and Universities.

ERIC Educational Resources Information Center

Qayoumi, Mohammad H.

2001-01-01

Presents the basic financial reporting elements of the Governmental Accounting Standards Board (GASB-35) for public colleges and universities, including statements of net assets and cash flow reporting. The GASB-35's impact on facilities managers is discussed. (GR)

A standardized sampling protocol for channel catfish in prairie streams

USGS Publications Warehouse

Vokoun, Jason C.; Rabeni, Charles F.

2001-01-01

Three alternative gears—an AC electrofishing raft, bankpoles, and a 15-hoop-net set—were used in a standardized manner to sample channel catfish Ictalurus punctatus in three prairie streams of varying size in three seasons. We compared these gears as to time required per sample, size selectivity, mean catch per unit effort (CPUE) among months, mean CPUE within months, effect of fluctuating stream stage, and sensitivity to population size. According to these comparisons, the 15-hoop-net set used during stable water levels in October had the most desirable characteristics. Using our catch data, we estimated the precision of CPUE and size structure by varying sample sizes for the 15-hoop-net set. We recommend that 11–15 repetitions of the 15-hoop-net set be used for most management activities. This standardized basic unit of effort will increase the precision of estimates and allow better comparisons among samples as well as increased confidence in management decisions.

Tools for Atmospheric Radiative Transfer: Streamer and FluxNet. Revised

NASA Technical Reports Server (NTRS)

Key, Jeffrey R.; Schweiger, Axel J.

1998-01-01

Two tools for the solution of radiative transfer problems are presented. Streamer is a highly flexible medium spectral resolution radiative transfer model based on the plane-parallel theory of radiative transfer. Capable of computing either fluxes or radiances, it is suitable for studying radiative processes at the surface or within the atmosphere and for the development of remote-sensing algorithms. FluxNet is a fast neural network-based implementation of Streamer for computing surface fluxes. It allows for a sophisticated treatment of radiative processes in the analysis of large data sets and potential integration into geophysical models where computational efficiency is an issue. Documentation and tools for the development of alternative versions of Fluxnet are available. Collectively, Streamer and FluxNet solve a wide variety of problems related to radiative transfer: Streamer provides the detail and sophistication needed to perform basic research on most aspects of complex radiative processes while the efficiency and simplicity of FluxNet make it ideal for operational use.

ABE NetNews, Volume 2.

ERIC Educational Resources Information Center

ABE NetNews, 2002

2002-01-01

These four newsletters focus on issues related to adult basic education and the challenges faced when teaching adult learners. The first issue introduces the LDA (Learning Disabilities Association) Learning Center, a private, nonprofit agency intended to maximize the potential of all people with learning disabilities or related learning…

VizieR Online Data Catalog: Catalog of Hγ measures (Petrie+ 1973)

NASA Astrophysics Data System (ADS)

Petrie, R. M.; Crampton, D.; Leir, A. Younger F.

2016-02-01

The catalog is a compilation of equivalent widths of H-γ for early-type stars, not only from published material but also from the numerous card files kept by R.M. Petrie. The luminosities of early-type stars through the measurement of the equivalent width of H-γ are relatively precise, although the early work was hampered by systematic errors in the absolute magnitude calibrations. In a number of cases, the values of the equivalent width for a given star differ slightly from publication to publication. There are three possible reasons for this: 1) The later publications may include measurements of additional spectra; 2) in some cases the values were included in the average; 3) some initial measures had not included the extremities of the very extensive wings of H-γ in the spectra of A stars. (2 data files).

Highly effective fungal inactivation in He+O2 atmospheric-pressure nonequilibrium plasmas

NASA Astrophysics Data System (ADS)

Xiong, Z.; Lu, X. P.; Feng, A.; Pan, Y.; Ostrikov, K.

2010-12-01

Highly effective (more than 99.9%) inactivation of a pathogenic fungus Candida albicans commonly found in oral, respiratory, digestive, and reproduction systems of a human body using atmospheric-pressure plasma jets sustained in He+O2 gas mixtures is reported. The inactivation is demonstrated in two fungal culture configurations with open (Petri dish without a cover) and restricted access to the atmosphere (Petri dish with a cover) under specific experimental conditions. It is shown that the fungal inactivation is remarkably more effective in the second configuration. This observation is supported by the scanning and transmission electron microscopy of the fungi before and after the plasma treatment. The inactivation mechanism explains the experimental observations under different experimental conditions and is consistent with the reports by other authors. The results are promising for the development of advanced health care applications.

Ovicidal activity of different concentrations of Pochonia chlamydosporia chlamydospores on Taenia taeniaeformis eggs.

PubMed

Braga, F R; Silva, A R; Carvalho, R O; Araújo, J V; Pinto, P S A

2011-03-01

Three concentrations of chlamydospores of the nematophagous fungus Pochonia chlamydosporia (1000, 10,000 and 20,000 per Petri dish) were evaluated in vitro on Taenia taeniaeformis eggs. Chlamydospores at each concentration were cultured in two different media: 2% water-agar (2%WA) and 2% corn-meal-agar (2%CMA). Taenia taeniaeformis eggs were plated in each chlamydospore concentration in 2%WA and 2%CMA (treated groups) and without fungus (control group). Eggs were removed from each Petri dish at intervals of 7, 14 and 21 days and classified according to ovicidal activity (type 1, type 2 and type 3 effects). Plates containing 2%CMA showed the highest percentages for type 3 effect (81.3%) on the 21st day of observation. A difference (P < 0.01) between the media 2%WA and 2%CMA for type 1 effect was observed only at a concentration of 1000 chlamydospores on the 7th day. There were differences (P < 0.01) between 2%WA and 2%CMA on the 14th and 21st days, at the concentration of 20,000 chlamydospores, for type 1 and type 3 effects. Regression curves for type 3 effect in 2%WA and 2%CMA at the tested concentrations showed higher ovicidal activity with increasing chlamydospore concentrations. Results indicate that, at concentrations of 1000, 10,000 and 20,000 per Petri dish, chlamydospores of P. chlamydosporia effectively destroyed T. taeniaeformis eggs and can be considered a potential biological control agent for this cestode.

A Study of Surface Temperatures, Clouds and Net Radiation

NASA Technical Reports Server (NTRS)

Dhuria, Harbans

1996-01-01

This study focused on the seasonal relationships and interactions of climate parameters such as the surface temperatures, net radiation, long wave flux, short wave flux, and clouds on a global basis. Five years of observations (December 1984 to November 1989) from the Earth Radiation Budget Experiment (ERBE) and the International Satellite Cloud Climatology Program (ISCCP) were used to study both seasonal variations and interannual variations by use of a basic radiation budget equation. In addition, the study was extended to include an analysis of the cloud forcing due El-Nino's impact on the ERBE parameters.

Selective carbon dioxide sorption by a new breathing three-dimensional Zn-MOF with Lewis basic nitrogen-rich channels.

PubMed

Kim, Hyun-Chul; Huh, Seong; Lee, Do Nam; Kim, Youngmee

2018-04-03

Lewis basic heteroatoms orderly located inside the well-defined channels of metal-organic frameworks (MOFs) are potentially ideal active sites for selective gas sorption and catalysis. To develop functional MOFs with Lewis basic sites inside channels, a new C2h-symmetric dicarboxylate-based bridging ligand, 3,3'-(pyrazine-2,5-diyl)dibenzoic acid (3,3'-PDBA), was prepared by a Suzuki coupling reaction. Subsequently, two new Zn-MOFs containing the C2h-symmetric 3,3'-PDBA bridging ligand and two different bis(pyridyl)-based pillars, 1,2-bis(4-pyridyl)ethane (bpa) or 1,2-bis(4-pyridyl)ethylene (bpe), were prepared through a thermal reaction in N,N-dimethylformamide (DMF). The resulting two Zn-MOFs of the general formula of three-dimensional (3D) [Zn2(μ4-3,3'-PDBA)2(μ2-bpa)]3·(DMF)5(H2O)13 (1) or 3D-like 2D [Zn2(μ4-3,3'-PDBA)2(μ2-bpe)]·(H2O) (2) displayed primitive cubic pcu net and 2D sql net, respectively. Both Zn-MOFs 1 and 2 contain uncoordinated Lewis basic pyrazinyl nitrogen atoms in the frameworks. The solvent-free 1 with flexible bpa linkers only showed a potential porosity of 15.9% by PLATON analysis. Zn-MOF 1 with openly accessible Lewis basic sites exhibited selective sorption of CO2 over N2, H2, and CH4 at low temperature. The adsorption and desorption isotherms for CO2 sorption at 196 K showed phenomenal hysteretic behaviour indicative of a breathing process through an adsorbate-discriminatory gate-opening process toward CO2 at a low gas pressure.

Remote Sensing and Capacity Building to Improve Food Security

NASA Astrophysics Data System (ADS)

Husak, G. J.; Funk, C. C.; Verdin, J. P.; Rowland, J.; Budde, M. E.

2012-12-01

The Famine Early Warning Systems Network (FEWS NET) is a U.S. Agency for International Development (USAID) supported project designed to monitor and anticipate food insecurity in the developing world, primarily Africa, Central America, the Caribbean and Central Asia. This is done through a network of partners involving U.S. government agencies, universities, country representatives, and partner institutions. This presentation will focus on the remotely sensed data used in FEWS NET activities and capacity building efforts designed to expand and enhance the use of FEWS NET tools and techniques. Remotely sensed data are of particular value in the developing world, where ground data networks and data reporting are limited. FEWS NET uses satellite based rainfall and vegetation greenness measures to monitor and assess food production conditions. Satellite rainfall estimates also drive crop models which are used in determining yield potential. Recent FEWS NET products also include estimates of actual evapotranspiration. Efforts are currently underway to assimilate these products into a single tool which would indicate areas experiencing abnormal conditions with implications for food production. FEWS NET is also involved in a number of capacity building activities. Two primary examples are the development of software and training of institutional partners in basic GIS and remote sensing. Software designed to incorporate rainfall station data with existing satellite-derived rainfall estimates gives users the ability to enhance satellite rainfall estimates or long-term means, resulting in gridded fields of rainfall that better reflect ground conditions. Further, this software includes a crop water balance model driven by the improved rainfall estimates. Finally, crop parameters, such as the planting date or length of growing period, can be adjusted by users to tailor the crop model to actual conditions. Training workshops in the use of this software, as well as basic GIS and remote sensing tools, are routinely conducted by FEWS NET representatives at host country meteorological and agricultural services. These institutions are then able to produce information that can more accurately inform food security decision making. Informed decision making reduces the risk associated with a given hazard. In the case of FEWS NET, this involves identification of shocks to food availability, allowing for the pre-positioning of aid to be available when a hazard strikes. Developing tools to incorporate better information in food production estimates and working closely with local staff trained in state-of-the-practice techniques results in a more informed decision making process, reducing the impacts of food security hazards.

7 CFR 1735.18 - Additional equity.

Code of Federal Regulations, 2010 CFR

2010-01-01

... AGRICULTURE GENERAL POLICIES, TYPES OF LOANS, LOAN REQUIREMENTS-TELECOMMUNICATIONS PROGRAM Loan Purposes and Basic Policies § 1735.18 Additional equity. If determined by the Administrator to be necessary for loan security, a borrower applying for an initial loan shall increase its net worth as a percentage of assets to...

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed Central

Maira, S M; Wurtz, J M; Wasylyk, B

1996-01-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation. Images PMID:8918463

Net (ERP/SAP2) one of the Ras-inducible TCFs, has a novel inhibitory domain with resemblance to the helix-loop-helix motif.

PubMed

Maira, S M; Wurtz, J M; Wasylyk, B

1996-11-01

The three ternary complex factors (TCFs), Net (ERP/ SAP-2), ELK-1 and SAP-1, are highly related ets oncogene family members that participate in the response of the cell to Ras and growth signals. Understanding the different roles of these factors will provide insights into how the signals result in coordinate regulation of the cell. We show that Net inhibits transcription under basal conditions, in which SAP-1a is inactive and ELK-1 stimulates. Repression is mediated by the NID, the Net Inhibitory Domain of about 50 amino acids, which autoregulates the Net protein and also inhibits when it is isolated in a heterologous fusion protein. Net is particularly sensitive to Ras activation. Ras activates Net through the C-domain, which is conserved between the three TCFs, and the NID is an efficient inhibitor of Ras activation. The NID, as well as more C-terminal sequences, inhibit DNA binding. Net is more refractory to DNA binding than the other TCFs, possibly due to the presence of multiple inhibitory elements. The NID may adopt a helix-loop-helix (HLH) structure, as evidenced by homology to other HLH motifs, structure predictions, model building and mutagenesis of critical residues. The sequence resemblance with myogenic factors suggested that Net may form complexes with the same partners. Indeed, we found that Net can interact in vivo with the basic HLH factor, E47. We propose that Net is regulated at the level of its latent DNA-binding activity by protein interactions and/or phosphorylation. Net may form complexes with HLH proteins as well as SRF on specific promotor sequences. The identification of the novel inhibitory domain provides a new inroad into exploring the different roles of the ternary complex factors in growth control and transformation.

Healthcare Information Technology Infrastructures in Turkey

PubMed Central

Yuksel, M.; Ertürkmen, G. L.; Kabak, Y.; Namli, T.; Yıldız, M. H.; Ay, Y.; Ceyhan, B.; Hülür, Ü.; Öztürk, H.; Atbakan, E.

2014-01-01

Summary Objectives The objective of this paper is to describe some of the major healthcare information technology (IT) infrastructures in Turkey, namely, Sağlık-Net (Turkish for “Health-Net”), the Centralized Hospital Appointment System, the Basic Health Statistics Module, the Core Resources Management System, and the e-prescription system of the Social Security Institution. International collaboration projects that are integrated with Sağlık-Net are also briefly summarized. Methods The authors provide a survey of the some of the major healthcare IT infrastructures in Turkey. Results Sağlık-Net has two main components: the National Health Information System (NHIS) and the Family Medicine Information System (FMIS). The NHIS is a nation-wide infrastructure for sharing patients’ Electronic Health Records (EHRs). So far, EHRs of 78.9 million people have been created in the NHIS. Similarly, family medicine is operational in the whole country via FMIS. Centralized Hospital Appointment System enables the citizens to easily make appointments in healthcare providers. Basic Health Statistics Module is used for collecting information about the health status, risks and indicators across the country. Core Resources Management System speeds up the flow of information between the headquarters and Provincial Health Directorates. The e-prescription system is linked with Sağlık-Net and seamlessly integrated with the healthcare provider information systems. Finally, Turkey is involved in several international projects for experience sharing and disseminating national developments. Conclusion With the introduction of the “Health Transformation Program” in 2003, a number of successful healthcare IT infrastructures have been developed in Turkey. Currently, work is going on to enhance and further improve their functionality. PMID:24853036

Formal modeling and analysis of ER-α associated Biological Regulatory Network in breast cancer.

PubMed

Khalid, Samra; Hanif, Rumeza; Tareen, Samar H K; Siddiqa, Amnah; Bibi, Zurah; Ahmad, Jamil

2016-01-01

Breast cancer (BC) is one of the leading cause of death among females worldwide. The increasing incidence of BC is due to various genetic and environmental changes which lead to the disruption of cellular signaling network(s). It is a complex disease in which several interlinking signaling cascades play a crucial role in establishing a complex regulatory network. The logical modeling approach of René Thomas has been applied to analyze the behavior of estrogen receptor-alpha (ER- α ) associated Biological Regulatory Network (BRN) for a small part of complex events that leads to BC metastasis. A discrete model was constructed using the kinetic logic formalism and its set of logical parameters were obtained using the model checking technique implemented in the SMBioNet software which is consistent with biological observations. The discrete model was further enriched with continuous dynamics by converting it into an equivalent Petri Net (PN) to analyze the logical parameters of the involved entities. In-silico based discrete and continuous modeling of ER- α associated signaling network involved in BC provides information about behaviors and gene-gene interaction in detail. The dynamics of discrete model revealed, imperative behaviors represented as cyclic paths and trajectories leading to pathogenic states such as metastasis. Results suggest that the increased expressions of receptors ER- α , IGF-1R and EGFR slow down the activity of tumor suppressor genes (TSGs) such as BRCA1, p53 and Mdm2 which can lead to metastasis. Therefore, IGF-1R and EGFR are considered as important inhibitory targets to control the metastasis in BC. The in-silico approaches allow us to increase our understanding of the functional properties of living organisms. It opens new avenues of investigations of multiple inhibitory targets (ER- α , IGF-1R and EGFR) for wet lab experiments as well as provided valuable insights in the treatment of cancers such as BC.

Postdefoliation ecosystem carbon and water flux and canopy growth dynamics in sagebrush steppe bunchgrass

USDA-ARS?s Scientific Manuscript database

Developing land-use practices that lead to sustainable net primary productivity in rangelands are important, but understanding their consequences to population and community processes is not often accounted for in basic ecosystem studies. Grazed and ungrazed upland ecosystems generally do not diffe...

77 FR 34915 - Notice of Data Availability Concerning Renewable Fuels Produced From Grain Sorghum Under the RFS...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-12

... alcohol manufacturing. Industry 325199 2869 Other basic organic chemical manufacturing. Industry 424690... fertilizer use, and energy use in feedstock processing and fuel production. The docket includes detailed... interval. Net agricultural emissions include impacts related to changes in crop inputs, such as fertilizer...

ABE NetNews, Volume 1.

ERIC Educational Resources Information Center

ABE NetNews, 2001

2001-01-01

These four newsletters focus on issues related to adult basic education and the challenges faced when teaching adult learners. The first issue looks at the characteristics of learning disabilities, providing information to help teachers determine whether a learner has a learning disability and who might be appropriately referred for testing. The…

76 FR 16570 - Interest Rate Risk

Federal Register 2010, 2011, 2012, 2013, 2014

2011-03-24

... greater than 10 years in the statement of financial condition of its most recent call report. For example..., asset valuation, or net economic value); Choose tests, such as interest rate shocks, that the credit... activities. For example, a credit union that offers basic share accounts, only short-term loans, i.e., no...

Reusable anaerobic system for microbiological studies - A concept

NASA Technical Reports Server (NTRS)

Murawczyk, C.

1971-01-01

Simple, low cost system consists of semirigid incubation chamber with clear Teflon window, airtight zipper and internal compartments for petri dishes or microbial plates. Device interests schools, medical laboratories, and manufacturers of biological and pharmaceutical supplies.

The Blue Bottle Experiment--Simple Demonstration of Self-Organization.

ERIC Educational Resources Information Center

Adamcikova, L'ubica; Sevcik, Peter

1998-01-01

Explains a way of observing pattern formation in the Blue Bottle chemistry demonstration by pouring a solution containing sodium hydroxide, glucose, and dye into a Petri dish and placing the dish on an overhead projector. (WRM)

Overhead Projector Demonstrations: A Classroom Demonstration of Aliphatic Substitution.

ERIC Educational Resources Information Center

Perina, Ivo; Mihanovic, Branka

1989-01-01

Presents a halogen substitution of an alkane using a compartmentalized Petri dish or Conway dish on an overhead projector. Provides methodology and several modifications for different reactions. Uses hexane, methyl orange, bromine, and silver nitrate. (MVL)

Swanson configures LMM for CARA-Petri Plant Experiment

NASA Image and Video Library

2014-05-05

ISS039-E-018472 (5 May 2014) --? NASA astronaut Steve Swanson, Expedition 39 flight engineer, works in the U.S. laboratory Destiny of the International Space Station, preparing the Light Microscopy Module (LMM) for a planet experiment.

Dispersal of Beauveria bassiana by the activity of nettle insects.

PubMed

Meyling, Nicolai V; Pell, Judith K; Eilenberg, Jørgen

2006-10-01

Recent studies have shown that the entomopathogenic fungus Beauveria bassiana occurs naturally on the phylloplanes of several plants, including nettles. Insects could, by their activity, be contributing to this inoculum by dispersing it from other sites. The potential of nettle aphids Microlophium carnosum and their predator Anthocoris nemorum to disperse conidia of B. bassiana from soil to nettles and from sporulating cadavers in the nettle canopy was investigated in laboratory experiments. In petri dish assays, aphids showed potential to distribute B. bassiana from soil to nettle leaves. Predators dispersed inoculum from both soil and cadavers to nettle leaves in petri dishes. In microcosms, aphids did not disperse B. bassiana from the soil or from cadavers confined in the canopy, but A. nemorum were able to transfer inoculum from soil into the nettle canopy and to distribute conidia from cryptic cadavers. In some instances, infections were initiated in aphids and predators as a consequence of dispersal.

Apex-4 for SpaceX CRS-10

NASA Image and Video Library

2017-02-16

APEX-04, or Advanced Plant EXperiments-04, is being prepared in a cold room in the Kennedy Space Center Processing Facility for SpaceX-10. Eric Morris from the cold stowage group places the APEX-04 science kits into the Double Cold Bag (DCB), which is a non-powered container that keeps the APEX petri plates at +4 degrees Celsius during launch and ascent. The cold bricks in the lower right of the photo are placed in the DCB prior to closure. Dr. Anna Lisa Paul of the University of Florida is the principal investigator for APEX-04. Apex-04 is an experiment involving Arabidopsis in petri plates inside the Veggie facility aboard the International Space Station. Since Arabidopsis is the genetic model of the plant world, it is a perfect sample organism for performing genetic studies in spaceflight. The experiment is the result of a grant from NASA’s Space Life and Physical Sciences division.

Adaptation of plastic surfaces for tissue culture by glow discharge.

PubMed Central

Amstein, C F; Hartman, P A

1975-01-01

Plastic petri dishes and microtitration plates were electrically charged by a glow discharge unit installed in a vacuum evaporator. Charged and uncharged plates, as well as plates commercially treated for tissue culture, were inoculated with Vero and BHK-21 cell lines; secondary cultures of monkey kidney, chicken lung, canine kidney, and embryonic bovine kidney; and primary chicken embryo fibroblasts and chicken lung cells. All cell cultures grew normally on petri plates charged with the covers open. Growth rate and cell density compared favorably with growth on the commercial tissue culture plates; cell growth was somewhat less dense, however, on plates charged with the covers closed. Charged plates could be sterilized by ultraviolet light and ethylene oxide with no adverse effects on cell growth. Cells inoculated onto plates charged up to 7 months before inoculation grew as well as on freshly charged plates. Images PMID:818106

Highly effective fungal inactivation in He+O{sub 2} atmospheric-pressure nonequilibrium plasmas

DOE Office of Scientific and Technical Information (OSTI.GOV)

Xiong, Z.; Lu, X. P.; Pan, Y.

2010-12-15

Highly effective (more than 99.9%) inactivation of a pathogenic fungus Candida albicans commonly found in oral, respiratory, digestive, and reproduction systems of a human body using atmospheric-pressure plasma jets sustained in He+O{sub 2} gas mixtures is reported. The inactivation is demonstrated in two fungal culture configurations with open (Petri dish without a cover) and restricted access to the atmosphere (Petri dish with a cover) under specific experimental conditions. It is shown that the fungal inactivation is remarkably more effective in the second configuration. This observation is supported by the scanning and transmission electron microscopy of the fungi before and aftermore » the plasma treatment. The inactivation mechanism explains the experimental observations under different experimental conditions and is consistent with the reports by other authors. The results are promising for the development of advanced health care applications.« less

NCWin — A Component Object Model (COM) for processing and visualizing NetCDF data

USGS Publications Warehouse

Liu, Jinxun; Chen, J.M.; Price, D.T.; Liu, S.

2005-01-01

NetCDF (Network Common Data Form) is a data sharing protocol and library that is commonly used in large-scale atmospheric and environmental data archiving and modeling. The NetCDF tool described here, named NCWin and coded with Borland C + + Builder, was built as a standard executable as well as a COM (component object model) for the Microsoft Windows environment. COM is a powerful technology that enhances the reuse of applications (as components). Environmental model developers from different modeling environments, such as Python, JAVA, VISUAL FORTRAN, VISUAL BASIC, VISUAL C + +, and DELPHI, can reuse NCWin in their models to read, write and visualize NetCDF data. Some Windows applications, such as ArcGIS and Microsoft PowerPoint, can also call NCWin within the application. NCWin has three major components: 1) The data conversion part is designed to convert binary raw data to and from NetCDF data. It can process six data types (unsigned char, signed char, short, int, float, double) and three spatial data formats (BIP, BIL, BSQ); 2) The visualization part is designed for displaying grid map series (playing forward or backward) with simple map legend, and displaying temporal trend curves for data on individual map pixels; and 3) The modeling interface is designed for environmental model development by which a set of integrated NetCDF functions is provided for processing NetCDF data. To demonstrate that the NCWin can easily extend the functions of some current GIS software and the Office applications, examples of calling NCWin within ArcGIS and MS PowerPoint for showing NetCDF map animations are given.

Learning the ropes at Richard B. Russell Dam: Net systems for medium head hydropower pumpback and generation fish sampling

DOE Office of Scientific and Technical Information (OSTI.GOV)

Schilt, C.R.; Vu, P.D.; Nestler, J.M.

1995-12-31

At Richard B. Russell Dam on the Savannah River we have been monitoring the magnitude (numbers and masses) and species compositions as well as possible survival of fish entrained in operation of four 85 MW Francis pump turbines. In this paper we review our progress in net design for hydropower application. We also discuss basic net handling and introduce a method for net management in a very turbulent tailrace. This report is meant to share what we have learned at Russell Dam in hopes that it will facilitate similar efforts elsewhere. The commercial fishing industry has evolved methods of netmore » construction and handling that may be applied, with appropriate modification, at dams. The nets we use are most appropriately called trawls in that they have the form of a long sock placed over the penstock or draft tube. These nets are superficially similar to those used in commercial trawling for fish. Important differences are that: (1) the net remains relatively stationary while the water moves through it, not vice versa; (2) water velocities and turbulence are much greater at dams than in commercial fishing operations and (3) mesh sizes are much smaller for environmental sampling than for commercial trawling. And while a fouled trawl may stop the boat that pulls it, the water passed in generation or pumpback (about 140 ft. head at Russell) is for all practical purposes unstoppable. Our nets fish in a very turbulent discharge at 7,000 cu. ft./sec/turbine. Their strength and their ability to pass water effectively under all possible operating conditions are primary concerns. Trawl length, mesh sizes, and hanging ratios are important factors. Although we have had setbacks (usually in the form of torn nets) as this study has developed, we have incrementally improved our net design and handling. We review our net failures and the solutions we have found thus far in both construction and handling.« less

Salient regions detection using convolutional neural networks and color volume

NASA Astrophysics Data System (ADS)

Liu, Guang-Hai; Hou, Yingkun

2018-03-01

Convolutional neural network is an important technique in machine learning, pattern recognition and image processing. In order to reduce the computational burden and extend the classical LeNet-5 model to the field of saliency detection, we propose a simple and novel computing model based on LeNet-5 network. In the proposed model, hue, saturation and intensity are utilized to extract depth cues, and then we integrate depth cues and color volume to saliency detection following the basic structure of the feature integration theory. Experimental results show that the proposed computing model outperforms some existing state-of-the-art methods on MSRA1000 and ECSSD datasets.

The research of .NET framework based on delegate of the LCE

NASA Astrophysics Data System (ADS)

Chen, Yi-peng

2011-10-01

Programmers realize LCE Enterprise services provided by NET framework when they develop applied VC# programming design language with component technology facing objects Lots of basic codes used to be compiled in the traditional programming design. However, nowadays this can be done just by adding corresponding character at class, interface, method, assembly with simple declarative program. This paper mainly expatiates the mechanism to realize LCE event services with delegate mode in C#. It also introduces the procedure of applying event class, event publisher, subscriber and client in LCE technology. It analyses the technology points of LCE based on delegate mode with popular language and practicing cases.

Centripetal Force on an Overhead Projector.

ERIC Educational Resources Information Center

Rheam, Harry

1995-01-01

Describes two simple demonstrations of an object moving in a straight line tangent to the circle if centripetal force is removed. Demonstrations use a pie plate and petri dish with ball bearings to illustrate the phenomena on an overhead projector. (LZ)

Sensitivity of Regional Climate to Deforestation in the Amazon Basin

NASA Technical Reports Server (NTRS)

Eltahir, Elfatih A. B.; Bras, Rafael L.

1994-01-01

The deforestation results in several adverse effect on the natural environment. The focus of this paper is on the effects of deforestation on land-surface processes and regional climate of the Amazon basin. In general, the effect of deforestation on climate are likely to depend on the scale of the defrosted area. In this study, we are interested in the effects due to deforestation of areas with a scale of about 250 km. Hence, a meso-scale climate model is used in performing numerical experiments on the sensitivity of regional climate to deforestation of areas with that size. It is found that deforestation results in less net surface radiation, less evaporation, less rainfall, and warmer surface temperature. The magnitude of the of the change in temperature is of the order 0.5 C, the magnitudes of the changes in the other variables are of the order of IO%. In order to verify some of he results of the numerical experiments, the model simulations of net surface radiation are compared to recent observations of net radiation over cleared and undisturbed forest in the Amazon. The results of the model and the observations agree in the following conclusion: the difference in net surface radiation between cleared and undisturbed forest is, almost, equally partioned between net solar radiation and net long-wave radiation. This finding contributes to our understanding of the basic physics in the deforestation problem.

Interconnected network motifs control podocyte morphology and kidney function.

PubMed

Azeloglu, Evren U; Hardy, Simon V; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y; Fang, Wei; Xiong, Huabao; Neves, Susana R; Jain, Mohit R; Li, Hong; Ma'ayan, Avi; Gordon, Ronald E; He, John Cijiang; Iyengar, Ravi

2014-02-04

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3',5'-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element-binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor-driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease.

Interconnected Network Motifs Control Podocyte Morphology and Kidney Function

PubMed Central

Azeloglu, Evren U.; Hardy, Simon V.; Eungdamrong, Narat John; Chen, Yibang; Jayaraman, Gomathi; Chuang, Peter Y.; Fang, Wei; Xiong, Huabao; Neves, Susana R.; Jain, Mohit R.; Li, Hong; Ma’ayan, Avi; Gordon, Ronald E.; He, John Cijiang; Iyengar, Ravi

2014-01-01

Podocytes are kidney cells with specialized morphology that is required for glomerular filtration. Diseases, such as diabetes, or drug exposure that causes disruption of the podocyte foot process morphology results in kidney pathophysiology. Proteomic analysis of glomeruli isolated from rats with puromycin-induced kidney disease and control rats indicated that protein kinase A (PKA), which is activated by adenosine 3′,5′-monophosphate (cAMP), is a key regulator of podocyte morphology and function. In podocytes, cAMP signaling activates cAMP response element–binding protein (CREB) to enhance expression of the gene encoding a differentiation marker, synaptopodin, a protein that associates with actin and promotes its bundling. We constructed and experimentally verified a β-adrenergic receptor–driven network with multiple feedback and feedforward motifs that controls CREB activity. To determine how the motifs interacted to regulate gene expression, we mapped multicompartment dynamical models, including information about protein subcellular localization, onto the network topology using Petri net formalisms. These computational analyses indicated that the juxtaposition of multiple feedback and feedforward motifs enabled the prolonged CREB activation necessary for synaptopodin expression and actin bundling. Drug-induced modulation of these motifs in diseased rats led to recovery of normal morphology and physiological function in vivo. Thus, analysis of regulatory motifs using network dynamics can provide insights into pathophysiology that enable predictions for drug intervention strategies to treat kidney disease. PMID:24497609

Proceedings of the First NASA Formal Methods Symposium

NASA Technical Reports Server (NTRS)

Denney, Ewen (Editor); Giannakopoulou, Dimitra (Editor); Pasareanu, Corina S. (Editor)

2009-01-01

Topics covered include: Model Checking - My 27-Year Quest to Overcome the State Explosion Problem; Applying Formal Methods to NASA Projects: Transition from Research to Practice; TLA+: Whence, Wherefore, and Whither; Formal Methods Applications in Air Transportation; Theorem Proving in Intel Hardware Design; Building a Formal Model of a Human-Interactive System: Insights into the Integration of Formal Methods and Human Factors Engineering; Model Checking for Autonomic Systems Specified with ASSL; A Game-Theoretic Approach to Branching Time Abstract-Check-Refine Process; Software Model Checking Without Source Code; Generalized Abstract Symbolic Summaries; A Comparative Study of Randomized Constraint Solvers for Random-Symbolic Testing; Component-Oriented Behavior Extraction for Autonomic System Design; Automated Verification of Design Patterns with LePUS3; A Module Language for Typing by Contracts; From Goal-Oriented Requirements to Event-B Specifications; Introduction of Virtualization Technology to Multi-Process Model Checking; Comparing Techniques for Certified Static Analysis; Towards a Framework for Generating Tests to Satisfy Complex Code Coverage in Java Pathfinder; jFuzz: A Concolic Whitebox Fuzzer for Java; Machine-Checkable Timed CSP; Stochastic Formal Correctness of Numerical Algorithms; Deductive Verification of Cryptographic Software; Coloured Petri Net Refinement Specification and Correctness Proof with Coq; Modeling Guidelines for Code Generation in the Railway Signaling Context; Tactical Synthesis Of Efficient Global Search Algorithms; Towards Co-Engineering Communicating Autonomous Cyber-Physical Systems; and Formal Methods for Automated Diagnosis of Autosub 6000.

Modeling and deadlock avoidance of automated manufacturing systems with multiple automated guided vehicles.

PubMed

Wu, Naiqi; Zhou, MengChu

2005-12-01

An automated manufacturing system (AMS) contains a number of versatile machines (or workstations), buffers, an automated material handling system (MHS), and is computer-controlled. An effective and flexible alternative for implementing MHS is to use automated guided vehicle (AGV) system. The deadlock issue in AMS is very important in its operation and has extensively been studied. The deadlock problems were separately treated for parts in production and transportation and many techniques were developed for each problem. However, such treatment does not take the advantage of the flexibility offered by multiple AGVs. In general, it is intractable to obtain maximally permissive control policy for either problem. Instead, this paper investigates these two problems in an integrated way. First we model an AGV system and part processing processes by resource-oriented Petri nets, respectively. Then the two models are integrated by using macro transitions. Based on the combined model, a novel control policy for deadlock avoidance is proposed. It is shown to be maximally permissive with computational complexity of O (n2) where n is the number of machines in AMS if the complexity for controlling the part transportation by AGVs is not considered. Thus, the complexity of deadlock avoidance for the whole system is bounded by the complexity in controlling the AGV system. An illustrative example shows its application and power.

Stochastic Coloured Petrinet Based Healthcare Infrastructure Interdependency Model

NASA Astrophysics Data System (ADS)

Nukavarapu, Nivedita; Durbha, Surya

2016-06-01

The Healthcare Critical Infrastructure (HCI) protects all sectors of the society from hazards such as terrorism, infectious disease outbreaks, and natural disasters. HCI plays a significant role in response and recovery across all other sectors in the event of a natural or manmade disaster. However, for its continuity of operations and service delivery HCI is dependent on other interdependent Critical Infrastructures (CI) such as Communications, Electric Supply, Emergency Services, Transportation Systems, and Water Supply System. During a mass casualty due to disasters such as floods, a major challenge that arises for the HCI is to respond to the crisis in a timely manner in an uncertain and variable environment. To address this issue the HCI should be disaster prepared, by fully understanding the complexities and interdependencies that exist in a hospital, emergency department or emergency response event. Modelling and simulation of a disaster scenario with these complexities would help in training and providing an opportunity for all the stakeholders to work together in a coordinated response to a disaster. The paper would present interdependencies related to HCI based on Stochastic Coloured Petri Nets (SCPN) modelling and simulation approach, given a flood scenario as the disaster which would disrupt the infrastructure nodes. The entire model would be integrated with Geographic information based decision support system to visualize the dynamic behaviour of the interdependency of the Healthcare and related CI network in a geographically based environment.

Requirements for Medical Modeling Languages

PubMed Central

van der Maas, Arnoud A.F.; Ter Hofstede, Arthur H.M.; Ten Hoopen, A. Johannes

2001-01-01

Objective: The development of tailor-made domain-specific modeling languages is sometimes desirable in medical informatics. Naturally, the development of such languages should be guided. The purpose of this article is to introduce a set of requirements for such languages and show their application in analyzing and comparing existing modeling languages. Design: The requirements arise from the practical experience of the authors and others in the development of modeling languages in both general informatics and medical informatics. The requirements initially emerged from the analysis of information modeling techniques. The requirements are designed to be orthogonal, i.e., one requirement can be violated without violation of the others. Results: The proposed requirements for any modeling language are that it be “formal” with regard to syntax and semantics, “conceptual,” “expressive,” “comprehensible,” “suitable,” and “executable.” The requirements are illustrated using both the medical logic modules of the Arden Syntax as a running example and selected examples from other modeling languages. Conclusion: Activity diagrams of the Unified Modeling Language, task structures for work flows, and Petri nets are discussed with regard to the list of requirements, and various tradeoffs are thus made explicit. It is concluded that this set of requirements has the potential to play a vital role in both the evaluation of existing domain-specific languages and the development of new ones. PMID:11230383

Usefulness of serum interleukin-18 in predicting cardiovascular mortality in patients with chronic kidney disease--systems and clinical approach.

PubMed

Formanowicz, Dorota; Wanic-Kossowska, Maria; Pawliczak, Elżbieta; Radom, Marcin; Formanowicz, Piotr

2015-12-16

The aim of this study was to check if serum interleukin-18 (IL-18) predicts 2-year cardiovascular mortality in patients at various stages of chronic kidney disease (CKD) and history of acute myocardial infarction (AMI) within the previous year. Diabetes mellitus was one of the key factors of exclusion. It was found that an increase in serum concentration of IL-18 above the cut-off point (1584.5 pg/mL) was characterized by 20.63-fold higher risk of cardiovascular deaths among studied patients. IL-18 serum concentration was found to be superior to the well-known cardiovascular risk parameters, like high sensitivity C-reactive protein (hsCRP), carotid intima media thickness (CIMT), glomerular filtration rate, albumins, ferritin, N-terminal prohormone of brain natriuretic peptide (NT-proBNP) in prognosis of cardiovascular mortality. The best predictive for IL-18 were 4 variables, such as CIMT, NT-proBNP, albumins and hsCRP, as they predicted its concentration at 89.5%. Concluding, IL-18 seems to be important indicator and predictor of cardiovascular death in two-year follow-up among non-diabetic patients suffering from CKD, with history of AMI in the previous year. The importance of IL-18 in the process of atherosclerotic plaque formation has been confirmed by systems analysis based on a formal model expressed in the language of Petri nets theory.

It's in the Bag: Digital Backpacks for Project-Based Learning

ERIC Educational Resources Information Center

Basham, James D.; Perry, Ernest; Meyer, Helen

2011-01-01

When it comes to technology, many schools know what they want. They want targeted and scalable solutions that enhance learning and meet the NETS.S. And the teachers in those schools want simple, strategic instructional frameworks for developing their students' basic and digital age skills while meeting diverse learning needs. But as many…

Stochastic architecture for Hopfield neural nets

NASA Technical Reports Server (NTRS)

Pavel, Sandy

1992-01-01

An expandable stochastic digital architecture for recurrent (Hopfield like) neural networks is proposed. The main features and basic principles of stochastic processing are presented. The stochastic digital architecture is based on a chip with n full interconnected neurons with a pipeline, bit processing structure. For large applications, a flexible way to interconnect many such chips is provided.