Formal modeling and analysis techniques for high level Petri nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. ^ There are two issues in using HLPNs—modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. ^ For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. ^ For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. ^ The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.^

Formal Modeling and Analysis Techniques for High Level Petri Nets

Petri Nets are a formal, graphical and executable modeling technique for the specification and analysis of concurrent and distributed systems and have been widely applied in computer science and many other engineering disciplines. Low level Petri nets are simple and useful for modeling control flows but not powerful enough to define data and system functionality. High level Petri nets (HLPNs) have been developed to support data and functionality definitions, such as using complex structured data as tokens and algebraic expressions as transition formulas. Compared to low level Petri nets, HLPNs result in compact system models that are easier to be understood. Therefore, HLPNs are more useful in modeling complex systems. There are two issues in using HLPNs - modeling and analysis. Modeling concerns the abstracting and representing the systems under consideration using HLPNs, and analysis deals with effective ways study the behaviors and properties of the resulting HLPN models. In this dissertation, several modeling and analysis techniques for HLPNs are studied, which are integrated into a framework that is supported by a tool. For modeling, this framework integrates two formal languages: a type of HLPNs called Predicate Transition Net (PrT Net) is used to model a system's behavior and a first-order linear time temporal logic (FOLTL) to specify the system's properties. The main contribution of this dissertation with regard to modeling is to develop a software tool to support the formal modeling capabilities in this framework. For analysis, this framework combines three complementary techniques, simulation, explicit state model checking and bounded model checking (BMC). Simulation is a straightforward and speedy method, but only covers some execution paths in a HLPN model. Explicit state model checking covers all the execution paths but suffers from the state explosion problem. BMC is a tradeoff as it provides a certain level of coverage while more efficient than explicit state model checking. The main contribution of this dissertation with regard to analysis is adapting BMC to analyze HLPN models and integrating the three complementary analysis techniques in a software tool to support the formal analysis capabilities in this framework. The SAMTools developed for this framework in this dissertation integrates three tools: PIPE+ for HLPNs behavioral modeling and simulation, SAMAT for hierarchical structural modeling and property specification, and PIPE+Verifier for behavioral verification.

Development of an open architecture motion control system

A multipurpose open architecture motion control system was developed with three platforms for control and monitoring. The Visual Basic user interface communicated with the operator and gave instructions to the electronic components. The first platform had a BASIC Stamp based controller and three stepping motors. The second platform had a controller, amplifiers and two DC servomotors. The third platform had a DSP module. In this study, each platform was used on machine tools either to move the table or to evaluate the incoming signal. The study indicated that by using advanced microcontrollers, which use high-level languages, motor controllers, DSPs (Digital Signal Processor) and microcomputers, the motion control of different systems could be realized in a short time. Although, the proposed systems had some limitations, their jobs were performed effectively. ^

A methodology for formally modeling and analyzing software architecture of mobile agent systems

A methodology for formally modeling and analyzing software architecture of mobile agent systems provides a solid basis to develop high quality mobile agent systems, and the methodology is helpful to study other distributed and concurrent systems as well. However, it is a challenge to provide the methodology because of the agent mobility in mobile agent systems.^ The methodology was defined from two essential parts of software architecture: a formalism to define the architectural models and an analysis method to formally verify system properties. The formalism is two-layer Predicate/Transition (PrT) nets extended with dynamic channels, and the analysis method is a hierarchical approach to verify models on different levels. The two-layer modeling formalism smoothly transforms physical models of mobile agent systems into their architectural models. Dynamic channels facilitate the synchronous communication between nets, and they naturally capture the dynamic architecture configuration and agent mobility of mobile agent systems. Component properties are verified based on transformed individual components, system properties are checked in a simplified system model, and interaction properties are analyzed on models composing from involved nets. Based on the formalism and the analysis method, this researcher formally modeled and analyzed a software architecture of mobile agent systems, and designed an architectural model of a medical information processing system based on mobile agents. The model checking tool SPIN was used to verify system properties such as reachability, concurrency and safety of the medical information processing system. ^ From successful modeling and analyzing the software architecture of mobile agent systems, the conclusion is that PrT nets extended with channels are a powerful tool to model mobile agent systems, and the hierarchical analysis method provides a rigorous foundation for the modeling tool. The hierarchical analysis method not only reduces the complexity of the analysis, but also expands the application scope of model checking techniques. The results of formally modeling and analyzing the software architecture of the medical information processing system show that model checking is an effective and an efficient way to verify software architecture. Moreover, this system shows a high level of flexibility, efficiency and low cost of mobile agent technologies. ^

Refinement methods for software architecture design using the software architecture model

Modern software systems are often large and complicated. To better understand, develop, and manage large software systems, researchers have studied software architectures that provide the top level overall structural design of software systems for the last decade. One major research focus on software architectures is formal architecture description languages, but most existing research focuses primarily on the descriptive capability and puts less emphasis on software architecture design methods and formal analysis techniques, which are necessary to develop correct software architecture design. ^ Refinement is a general approach of adding details to a software design. A formal refinement method can further ensure certain design properties. This dissertation proposes refinement methods, including a set of formal refinement patterns and complementary verification techniques, for software architecture design using Software Architecture Model (SAM), which was developed at Florida International University. First, a general guideline for software architecture design in SAM is proposed. Second, specification construction through property-preserving refinement patterns is discussed. The refinement patterns are categorized into connector refinement, component refinement and high-level Petri nets refinement. These three levels of refinement patterns are applicable to overall system interaction, architectural components, and underlying formal language, respectively. Third, verification after modeling as a complementary technique to specification refinement is discussed. Two formal verification tools, the Stanford Temporal Prover (STeP) and the Simple Promela Interpreter (SPIN), are adopted into SAM to develop the initial models. Fourth, formalization and refinement of security issues are studied. A method for security enforcement in SAM is proposed. The Role-Based Access Control model is formalized using predicate transition nets and Z notation. The patterns of enforcing access control and auditing are proposed. Finally, modeling and refining a life insurance system is used to demonstrate how to apply the refinement patterns for software architecture design using SAM and how to integrate the access control model. ^ The results of this dissertation demonstrate that a refinement method is an effective way to develop a high assurance system. The method developed in this dissertation extends existing work on modeling software architectures using SAM and makes SAM a more usable and valuable formal tool for software architecture design. ^

A semantic paradigm for intelligent data access

An implementation of Sem-ODB—a database management system based on the Semantic Binary Model is presented. A metaschema of Sem-ODB database as well as the top-level architecture of the database engine is defined. A new benchmarking technique is proposed which allows databases built on different database models to compete fairly. This technique is applied to show that Sem-ODB has excellent efficiency comparing to a relational database on a certain class of database applications. A new semantic benchmark is designed which allows evaluation of the performance of the features characteristic of semantic database applications. An application used in the benchmark represents a class of problems requiring databases with sparse data, complex inheritances and many-to-many relations. Such databases can be naturally accommodated by semantic model. A fixed predefined implementation is not enforced allowing the database designer to choose the most efficient structures available in the DBMS tested. The results of the benchmark are analyzed. ^ A new high-level querying model for semantic databases is defined. It is proven adequate to serve as an efficient native semantic database interface, and has several advantages over the existing interfaces. It is optimizable and parallelizable, supports the definition of semantic userviews and the interoperability of semantic databases with other data sources such as World Wide Web, relational, and object-oriented databases. The query is structured as a semantic database schema graph with interlinking conditionals. The query result is a mini-database, accessible in the same way as the original database. The paradigm supports and utilizes the rich semantics and inherent ergonomics of semantic databases. ^ The analysis and high-level design of a system that exploits the superiority of the Semantic Database Model to other data models in expressive power and ease of use to allow uniform access to heterogeneous data sources such as semantic databases, relational databases, web sites, ASCII files, and others via a common query interface is presented. The Sem-ODB engine is used to control all the data sources combined under a unified semantic schema. A particular application of the system to provide an ODBC interface to the WWW as a data source is discussed. ^

An integrated framework for ensuring the quality of software design

Software development is an extremely complex process, during which human errors are introduced and result in faulty software systems. It is highly desirable and important that these errors can be prevented and detected as early as possible. Software architecture design is a high-level system description, which embodies many system features and properties that are eventually implemented in the final operational system. Therefore, methods for modeling and analyzing software architecture descriptions can help prevent and reveal human errors and thus improve software quality. Furthermore, if an analyzed software architecture description can be used to derive a partial software implementation, especially when the derivation can be automated, significant benefits can be gained with regard to both the system quality and productivity. This dissertation proposes a framework for an integrated analysis on both of the design and implementation. To ensure the desirable properties of the architecture model, we apply formal verification by using the model checking technique. To ensure the desirable properties of the implementation, we develop a methodology and the associated tool to translate an architecture specification into an implementation written in the combination of Arch-Java/Java/AspectJ programming languages. The translation is semi-automatic so that many manual programming errors can be prevented. Furthermore, the translation inserting monitoring code into the implementation such that runtime verification can be performed, this provides additional assurance for the quality of the implementation. Moreover, validations for the translations from architecture model to program are provided. Finally, several case studies are experimented and presented.

High natural gene expression variation in the reef-building coral Acropora millepora: potential for acclimative and adaptive plasticity

Background: Ecosystems worldwide are suffering the consequences of anthropogenic impact. The diverse ecosystem of coral reefs, for example, are globally threatened by increases in sea surface temperatures due to global warming. Studies to date have focused on determining genetic diversity, the sequence variability of genes in a species, as a proxy to estimate and predict the potential adaptive response of coral populations to environmental changes linked to climate changes. However, the examination of natural gene expression variation has received less attention. This variation has been implicated as an important factor in evolutionary processes, upon which natural selection can act. Results: We acclimatized coral nubbins from six colonies of the reef-building coral Acropora millepora to a common garden in Heron Island (Great Barrier Reef, GBR) for a period of four weeks to remove any site-specific environmental effects on the physiology of the coral nubbins. By using a cDNA microarray platform, we detected a high level of gene expression variation, with 17% (488) of the unigenes differentially expressed across coral nubbins of the six colonies (jsFDR-corrected, p < 0.01). Among the main categories of biological processes found differentially expressed were transport, translation, response to stimulus, oxidation-reduction processes, and apoptosis. We found that the transcriptional profiles did not correspond to the genotype of the colony characterized using either an intron of the carbonic anhydrase gene or microsatellite loci markers. Conclusion: Our results provide evidence of the high inter-colony variation in A. millepora at the transcriptomic level grown under a common garden and without a correspondence with genotypic identity. This finding brings to our attention the importance of taking into account natural variation between reef corals when assessing experimental gene expression differences. The high transcriptional variation detected in this study is interpreted and discussed within the context of adaptive potential and phenotypic plasticity of reef corals. Whether this variation will allow coral reefs to survive to current challenges remains unknown.

Hybrid power system intelligent operation and protection involving distributed architectures and pulsed loads

Efficient and reliable techniques for power delivery and utilization are needed to account for the increased penetration of renewable energy sources in electric power systems. Such methods are also required for current and future demands of plug-in electric vehicles and high-power electronic loads. Distributed control and optimal power network architectures will lead to viable solutions to the energy management issue with high level of reliability and security. This dissertation is aimed at developing and verifying new techniques for distributed control by deploying DC microgrids, involving distributed renewable generation and energy storage, through the operating AC power system. To achieve the findings of this dissertation, an energy system architecture was developed involving AC and DC networks, both with distributed generations and demands. The various components of the DC microgrid were designed and built including DC-DC converters, voltage source inverters (VSI) and AC-DC rectifiers featuring novel designs developed by the candidate. New control techniques were developed and implemented to maximize the operating range of the power conditioning units used for integrating renewable energy into the DC bus. The control and operation of the DC microgrids in the hybrid AC/DC system involve intelligent energy management. Real-time energy management algorithms were developed and experimentally verified. These algorithms are based on intelligent decision-making elements along with an optimization process. This was aimed at enhancing the overall performance of the power system and mitigating the effect of heavy non-linear loads with variable intensity and duration. The developed algorithms were also used for managing the charging/discharging process of plug-in electric vehicle emulators. The protection of the proposed hybrid AC/DC power system was studied. Fault analysis and protection scheme and coordination, in addition to ideas on how to retrofit currently available protection concepts and devices for AC systems in a DC network, were presented. A study was also conducted on the effect of changing the distribution architecture and distributing the storage assets on the various zones of the network on the system's dynamic security and stability. A practical shipboard power system was studied as an example of a hybrid AC/DC power system involving pulsed loads. Generally, the proposed hybrid AC/DC power system, besides most of the ideas, controls and algorithms presented in this dissertation, were experimentally verified at the Smart Grid Testbed, Energy Systems Research Laboratory. All the developments in this dissertation were experimentally verified at the Smart Grid Testbed.

Hybrid Power System Intelligent Operation and Protection Involving Distributed Architectures and Pulsed Loads

Efficient and reliable techniques for power delivery and utilization are needed to account for the increased penetration of renewable energy sources in electric power systems. Such methods are also required for current and future demands of plug-in electric vehicles and high-power electronic loads. Distributed control and optimal power network architectures will lead to viable solutions to the energy management issue with high level of reliability and security. This dissertation is aimed at developing and verifying new techniques for distributed control by deploying DC microgrids, involving distributed renewable generation and energy storage, through the operating AC power system. To achieve the findings of this dissertation, an energy system architecture was developed involving AC and DC networks, both with distributed generations and demands. The various components of the DC microgrid were designed and built including DC-DC converters, voltage source inverters (VSI) and AC-DC rectifiers featuring novel designs developed by the candidate. New control techniques were developed and implemented to maximize the operating range of the power conditioning units used for integrating renewable energy into the DC bus. The control and operation of the DC microgrids in the hybrid AC/DC system involve intelligent energy management. Real-time energy management algorithms were developed and experimentally verified. These algorithms are based on intelligent decision-making elements along with an optimization process. This was aimed at enhancing the overall performance of the power system and mitigating the effect of heavy non-linear loads with variable intensity and duration. The developed algorithms were also used for managing the charging/discharging process of plug-in electric vehicle emulators. The protection of the proposed hybrid AC/DC power system was studied. Fault analysis and protection scheme and coordination, in addition to ideas on how to retrofit currently available protection concepts and devices for AC systems in a DC network, were presented. A study was also conducted on the effect of changing the distribution architecture and distributing the storage assets on the various zones of the network on the system’s dynamic security and stability. A practical shipboard power system was studied as an example of a hybrid AC/DC power system involving pulsed loads. Generally, the proposed hybrid AC/DC power system, besides most of the ideas, controls and algorithms presented in this dissertation, were experimentally verified at the Smart Grid Testbed, Energy Systems Research Laboratory. All the developments in this dissertation were experimentally verified at the Smart Grid Testbed.