Web-based report generators, data visualization, and Web-to-database connectivity

Because some Web users will be able to design a template to visualize information from scratch, while other users need to automatically visualize information by changing some parameters, providing different levels of customization of the information is a desirable goal. Our system allows the automatic generation of visualizations given the semantics of the data, and the static or pre-specified visualization by creating an interface language. We address information visualization taking into consideration the Web, where the presentation of the retrieved information is a challenge. ^ We provide a model to narrow the gap between the user's way of expressing queries and database manipulation languages (SQL) without changing the system itself thus improving the query specification process. We develop a Web interface model that is integrated with the HTML language to create a powerful language that facilitates the construction of Web-based database reports. ^ As opposed to other papers, this model offers a new way of exploring databases focusing on providing Web connectivity to databases with minimal or no result buffering, formatting, or extra programming. We describe how to easily connect the database to the Web. In addition, we offer an enhanced way on viewing and exploring the contents of a database, allowing users to customize their views depending on the contents and the structure of the data. Current database front-ends typically attempt to display the database objects in a flat view making it difficult for users to grasp the contents and the structure of their result. Our model narrows the gap between databases and the Web. ^ The overall objective of this research is to construct a model that accesses different databases easily across the net and generates SQL, forms, and reports across all platforms without requiring the developer to code a complex application. This increases the speed of development. In addition, using only the Web browsers, the end-user can retrieve data from databases remotely to make necessary modifications and manipulations of data using the Web formatted forms and reports, independent of the platform, without having to open different applications, or learn to use anything but their Web browser. We introduce a strategic method to generate and construct SQL queries, enabling inexperienced users that are not well exposed to the SQL world to build syntactically and semantically a valid SQL query and to understand the retrieved data. The generated SQL query will be validated against the database schema to ensure harmless and efficient SQL execution. (Abstract shortened by UMI.)^

A realtime Internet-based quality control application for hurricane surface wind observations

This thesis chronicles the design and implementation of a Internet/Intranet and database based application for the quality control of hurricane surface wind observations. A quality control session consists of selecting desired observation types to be viewed and determining a storm track based time window for viewing the data. All observations of the selected types are then plotted in a storm relative view for the chosen time window and geography is positioned for the storm-center time about which an objective analysis can be performed. Users then make decisions about data validity through visual nearest-neighbor comparison and inspection. The project employed an Object Oriented iterative development method from beginning to end and its implementation primarily features the Java programming language. ^

Signal processing of physiological signals for automated assessment of stress in computer users

The need to provide computers with the ability to distinguish the affective state of their users is a major requirement for the practical implementation of affective computing concepts. This dissertation proposes the application of signal processing methods on physiological signals to extract from them features that can be processed by learning pattern recognition systems to provide cues about a person's affective state. In particular, combining physiological information sensed from a user's left hand in a non-invasive way with the pupil diameter information from an eye-tracking system may provide a computer with an awareness of its user's affective responses in the course of human-computer interactions. In this study an integrated hardware-software setup was developed to achieve automatic assessment of the affective status of a computer user. A computer-based "Paced Stroop Test" was designed as a stimulus to elicit emotional stress in the subject during the experiment. Four signals: the Galvanic Skin Response (GSR), the Blood Volume Pulse (BVP), the Skin Temperature (ST) and the Pupil Diameter (PD), were monitored and analyzed to differentiate affective states in the user. Several signal processing techniques were applied on the collected signals to extract their most relevant features. These features were analyzed with learning classification systems, to accomplish the affective state identification. Three learning algorithms: Naïve Bayes, Decision Tree and Support Vector Machine were applied to this identification process and their levels of classification accuracy were compared. The results achieved indicate that the physiological signals monitored do, in fact, have a strong correlation with the changes in the emotional states of the experimental subjects. These results also revealed that the inclusion of pupil diameter information significantly improved the performance of the emotion recognition system. ^

Expanding guitar production techniques: Building the Guitar Application Toolkit (GATK)

The purpose of this thesis was to build the Guitar Application ToolKit (GATK), a series of applications used to expand the sonic capabilities of the acoustic/electric stereo guitar. Furthermore, the goal of the GATK was to extend improvisational capabilities and the compositional techniques generated by this innovative instrument. ^ During the GATK creation process, the current production guitar techniques and overall sonic result were enhanced by planning and implementing a personalized electro-acoustic performance set up, designing custom-made performance interfaces, creating interactive compositional strategies, crafting non-standardized sounds, and controlling various music parameters in real-time using the Max/MSP programming environment. ^ This was the fast thesis project of its kind. It is expected that this thesis will be useful as a reference paper for electronic musicians and music technology students; as a product demonstration for companies that manufacture the relevant software; and as a personal portfolio for future technology related jobs. ^

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.

Enabling adaptability in service aggregates using transparent shaping techniques

Distributed applications are exposed as reusable components that are dynamically discovered and integrated to create new applications. These new applications, in the form of aggregate services, are vulnerable to failure due to the autonomous and distributed nature of their integrated components. This vulnerability creates the need for adaptability in aggregate services. The need for adaptation is accentuated for complex long-running applications as is found in scientific Grid computing, where distributed computing nodes may participate to solve computation and data-intensive problems. Such applications integrate services for coordinated problem solving in areas such as Bioinformatics. For such applications, when a constituent service fails, the application fails, even though there are other nodes that can substitute for the failed service. This concern is not addressed in the specification of high-level composition languages such as that of the Business Process Execution Language (BPEL). We propose an approach to transparently autonomizing existing BPEL processes in order to make them modifiable at runtime and more resilient to the failures in their execution environment. By transparent introduction of adaptive behavior, adaptation preserves the original business logic of the aggregate service and does not tangle the code for adaptive behavior with that of the aggregate service. The major contributions of this dissertation are: first, we assessed the effectiveness of BPEL language support in developing adaptive mechanisms. As a result, we identified the strengths and limitations of BPEL and came up with strategies to address those limitations. Second, we developed a technique to enhance existing BPEL processes transparently in order to support dynamic adaptation. We proposed a framework which uses transparent shaping and generative programming to make BPEL processes adaptive. Third, we developed a technique to dynamically discover and bind to substitute services. Our technique was evaluated and the result showed that dynamic utilization of components improves the flexibility of adaptive BPEL processes. Fourth, we developed an extensible policy-based technique to specify how to handle exceptional behavior. We developed a generic component that introduces adaptive behavior for multiple BPEL processes. Fifth, we identify ways to apply our work to facilitate adaptability in composite Grid services.

Bioinformatic analysis for exploring relationships between genes and gene products

To carry out their specific roles in the cell, genes and gene products often work together in groups, forming many relationships among themselves and with other molecules. Such relationships include physical protein-protein interaction relationships, regulatory relationships, metabolic relationships, genetic relationships, and much more. With advances in science and technology, some high throughput technologies have been developed to simultaneously detect tens of thousands of pairwise protein-protein interactions and protein-DNA interactions. However, the data generated by high throughput methods are prone to noise. Furthermore, the technology itself has its limitations, and cannot detect all kinds of relationships between genes and their products. Thus there is a pressing need to investigate all kinds of relationships and their roles in a living system using bioinformatic approaches, and is a central challenge in Computational Biology and Systems Biology. This dissertation focuses on exploring relationships between genes and gene products using bioinformatic approaches. Specifically, we consider problems related to regulatory relationships, protein-protein interactions, and semantic relationships between genes. A regulatory element is an important pattern or "signal", often located in the promoter of a gene, which is used in the process of turning a gene "on" or "off". Predicting regulatory elements is a key step in exploring the regulatory relationships between genes and gene products. In this dissertation, we consider the problem of improving the prediction of regulatory elements by using comparative genomics data. With regard to protein-protein interactions, we have developed bioinformatics techniques to estimate support for the data on these interactions. While protein-protein interactions and regulatory relationships can be detected by high throughput biological techniques, there is another type of relationship called semantic relationship that cannot be detected by a single technique, but can be inferred using multiple sources of biological data. The contributions of this thesis involved the development and application of a set of bioinformatic approaches that address the challenges mentioned above. These included (i) an EM-based algorithm that improves the prediction of regulatory elements using comparative genomics data, (ii) an approach for estimating the support of protein-protein interaction data, with application to functional annotation of genes, (iii) a novel method for inferring functional network of genes, and (iv) techniques for clustering genes using multi-source data.

Realization of Differentiated Quality of Service for Wideband Code Division Multiple Access Core Network

The development of 3G (the 3rd generation telecommunication) value-added services brings higher requirements of Quality of Service (QoS). Wideband Code Division Multiple Access (WCDMA) is one of three 3G standards, and enhancement of QoS for WCDMA Core Network (CN) becomes more and more important for users and carriers. The dissertation focuses on enhancement of QoS for WCDMA CN. The purpose is to realize the DiffServ (Differentiated Services) model of QoS for WCDMA CN. Based on the parallelism characteristic of Network Processors (NPs), the NP programming model is classified as Pool of Threads (POTs) and Hyper Task Chaining (HTC). In this study, an integrated programming model that combines both of the two models was designed. This model has highly efficient and flexible features, and also solves the problems of sharing conflicts and packet ordering. We used this model as the programming model to realize DiffServ QoS for WCDMA CN. ^ The realization mechanism of the DiffServ model mainly consists of buffer management, packet scheduling and packet classification algorithms based on NPs. First, we proposed an adaptive buffer management algorithm called Packet Adaptive Fair Dropping (PAFD), which takes into consideration of both fairness and throughput, and has smooth service curves. Then, an improved packet scheduling algorithm called Priority-based Weighted Fair Queuing (PWFQ) was introduced to ensure the fairness of packet scheduling and reduce queue time of data packets. At the same time, the delay and jitter are also maintained in a small range. Thirdly, a multi-dimensional packet classification algorithm called Classification Based on Network Processors (CBNPs) was designed. It effectively reduces the memory access and storage space, and provides less time and space complexity. ^ Lastly, an integrated hardware and software system of the DiffServ model of QoS for WCDMA CN was proposed. It was implemented on the NP IXP2400. According to the corresponding experiment results, the proposed system significantly enhanced QoS for WCDMA CN. It extensively improves consistent response time, display distortion and sound image synchronization, and thus increases network efficiency and saves network resource.^

Towards simulation and emulation of large-scale computer networks

Developing analytical models that can accurately describe behaviors of Internet-scale networks is difficult. This is due, in part, to the heterogeneous structure, immense size and rapidly changing properties of today's networks. The lack of analytical models makes large-scale network simulation an indispensable tool for studying immense networks. However, large-scale network simulation has not been commonly used to study networks of Internet-scale. This can be attributed to three factors: 1) current large-scale network simulators are geared towards simulation research and not network research, 2) the memory required to execute an Internet-scale model is exorbitant, and 3) large-scale network models are difficult to validate. This dissertation tackles each of these problems. ^ First, this work presents a method for automatically enabling real-time interaction, monitoring, and control of large-scale network models. Network researchers need tools that allow them to focus on creating realistic models and conducting experiments. However, this should not increase the complexity of developing a large-scale network simulator. This work presents a systematic approach to separating the concerns of running large-scale network models on parallel computers and the user facing concerns of configuring and interacting with large-scale network models. ^ Second, this work deals with reducing memory consumption of network models. As network models become larger, so does the amount of memory needed to simulate them. This work presents a comprehensive approach to exploiting structural duplications in network models to dramatically reduce the memory required to execute large-scale network experiments. ^ Lastly, this work addresses the issue of validating large-scale simulations by integrating real protocols and applications into the simulation. With an emulation extension, a network simulator operating in real-time can run together with real-world distributed applications and services. As such, real-time network simulation not only alleviates the burden of developing separate models for applications in simulation, but as real systems are included in the network model, it also increases the confidence level of network simulation. This work presents a scalable and flexible framework to integrate real-world applications with real-time simulation.^

Leveraging symbiotic relationships for emulation of computer networks

The lack of analytical models that can accurately describe large-scale networked systems makes empirical experimentation indispensable for understanding complex behaviors. Research on network testbeds for testing network protocols and distributed services, including physical, emulated, and federated testbeds, has made steady progress. Although the success of these testbeds is undeniable, they fail to provide: 1) scalability, for handling large-scale networks with hundreds or thousands of hosts and routers organized in different scenarios, 2) flexibility, for testing new protocols or applications in diverse settings, and 3) inter-operability, for combining simulated and real network entities in experiments. This dissertation tackles these issues in three different dimensions. First, we present SVEET, a system that enables inter-operability between real and simulated hosts. In order to increase the scalability of networks under study, SVEET enables time-dilated synchronization between real hosts and the discrete-event simulator. Realistic TCP congestion control algorithms are implemented in the simulator to allow seamless interactions between real and simulated hosts. SVEET is validated via extensive experiments and its capabilities are assessed through case studies involving real applications. Second, we present PrimoGENI, a system that allows a distributed discrete-event simulator, running in real-time, to interact with real network entities in a federated environment. PrimoGENI greatly enhances the flexibility of network experiments, through which a great variety of network conditions can be reproduced to examine what-if questions. Furthermore, PrimoGENI performs resource management functions, on behalf of the user, for instantiating network experiments on shared infrastructures. Finally, to further increase the scalability of network testbeds to handle large-scale high-capacity networks, we present a novel symbiotic simulation approach. We present SymbioSim, a testbed for large-scale network experimentation where a high-performance simulation system closely cooperates with an emulation system in a mutually beneficial way. On the one hand, the simulation system benefits from incorporating the traffic metadata from real applications in the emulation system to reproduce the realistic traffic conditions. On the other hand, the emulation system benefits from receiving the continuous updates from the simulation system to calibrate the traffic between real applications. Specific techniques that support the symbiotic approach include: 1) a model downscaling scheme that can significantly reduce the complexity of the large-scale simulation model, resulting in an efficient emulation system for modulating the high-capacity network traffic between real applications; 2) a queuing network model for the downscaled emulation system to accurately represent the network effects of the simulated traffic; and 3) techniques for reducing the synchronization overhead between the simulation and emulation systems.

Phylogenetic analysis of within -host serially-sampled viral data

The primary goal of this dissertation is the study of patterns of viral evolution inferred from serially-sampled sequence data, i.e., sequence data obtained from strains isolated at consecutive time points from a single patient or host. RNA viral populations have an extremely high genetic variability, largely due to their astronomical population sizes within host systems, high replication rate, and short generation time. It is this aspect of their evolution that demands special attention and a different approach when studying the evolutionary relationships of serially-sampled sequence data. New methods that analyze serially-sampled data were developed shortly after a groundbreaking HIV-1 study of several patients from which viruses were isolated at recurring intervals over a period of 10 or more years. These methods assume a tree-like evolutionary model, while many RNA viruses have the capacity to exchange genetic material with one another using a process called recombination. ^ A genealogy involving recombination is best described by a network structure. A more general approach was implemented in a new computational tool, Sliding MinPD, one that is mindful of the sampling times of the input sequences and that reconstructs the viral evolutionary relationships in the form of a network structure with implicit representations of recombination events. The underlying network organization reveals unique patterns of viral evolution and could help explain the emergence of disease-associated mutants and drug-resistant strains, with implications for patient prognosis and treatment strategies. In order to comprehensively test the developed methods and to carry out comparison studies with other methods, synthetic data sets are critical. Therefore, appropriate sequence generators were also developed to simulate the evolution of serially-sampled recombinant viruses, new and more through evaluation criteria for recombination detection methods were established, and three major comparison studies were performed. The newly developed tools were also applied to "real" HIV-1 sequence data and it was shown that the results represented within an evolutionary network structure can be interpreted in biologically meaningful ways. ^

A ROS-based Workspace Control and Trajectory Planner for a seven degrees of freedom Robotic arm

In this Bachelor Thesis I want to provide readers with tools and scripts for the control of a 7DOF manipulator, backed up by some theory of Robotics and Computer Science, in order to better contextualize the work done. In practice, we will see most common software, and developing environments, used to cope with our task: these include ROS, along with visual simulation by VREP and RVIZ, and an almost "stand-alone" ROS extension called MoveIt!, a very complete programming interface for trajectory planning and obstacle avoidance. As we will better appreciate and understand in the introduction chapter, the capability of detecting collision objects through a camera sensor, and re-plan to the desired end-effector pose, are not enough. In fact, this work is implemented in a more complex system, where recognition of particular objects is needed. Through a package of ROS and customized scripts, a detailed procedure will be provided on how to distinguish a particular object, retrieve its reference frame with respect to a known one, and then allow navigation to that target. Together with technical details, the aim is also to report working scripts and a specific appendix (A) you can refer to, if desiring to put things together.

Personal Storytelling : Using Natural Language Generation for Children with Complex Communication Needs, in the Wild...

Acknowledgements The authors thank the children, their parents and school staff, who participated in this research, and who so willingly gave us their time, help and support. They also thank Steven Knox and Alan Clelland for their work on programming the mobile phone application. Additional thanks to DynaVox Inc. for supplying the Vmax communication devices to run our system on and Sensory Software Ltd for supplying us with their AAC software. This research was supported by the Research Council UKs Digittal Economy Programme and EPSRC (Grant numbers EP/F067151/1, EP/F066880/1, EP/E011764/1, EP/H022376/1, and EP/H022570 /1).

Learning Meta-Descriptions of the FOAF Network

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FdDCA : A Novel Fuzzy Deterministic Dendritic Cell Algorithm

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