Extending the MVC Design Pattern towards a Task-Oriented Development Approach for Pervasive Computing Applications

This paper addresses the implementation of pervasive Java Web applications using a development approach that is based on the Model-View- Controller (MVC) design pattern. We combine the MVC methodology with a hierarchical task-based state transition model in order to achieve the distinction between the task state and the view state of an application. More precisely, we propose to add a device-independent TaskStateBean and a device-specific ViewStateBean for each task state as an extension to the J2EE Service to Worker design pattern. Furthermore, we suggest representing the task state and view state transition models as finite state automata in two sets of XML files

An object-oriented framework to organize genomic data

Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data

An object-oriented framework to organize genomic data

Bioinformatics resources should provide simple and flexible support for genomics research. A huge amount of gene mapping data, micro-array expression data, expressed sequence tags (EST), BAC sequence data and genome sequence data are already, or will soon be available for a number of livestock species. These species will have different requirements compared to typical biomedical model organisms and will need an informatics framework to deal with the data. In term of exploring complex-intertwined genomic data, the way to organize them will be addressed in this study. Therefore, we investigated two issues in this study: one is an independent informatics framework including both back end and front end; another is how an informatics framework simplifies the user interface to explore data. We have developed a fundamental informatics framework that makes it easy to organize and manipulate the complex relations between genomic data, and allow for query results to be presented via a user friendly web interface. A genome object-oriented framework (GOOF) was proposed with object-oriented Java technology and is independent of any database system. This framework seamlessly links the database system and web presentation components. The data models of GOOF collect the data relationships in order to provide users with access to relations across different types of data, meaning that users avoid constructing queries within the interface layer. Moreover, the module-based interface provided by GOOF could allow different users to access data in different interfaces and ways. In another words, GOOF not only gives a whole solution to informatics infrastructure, but also simplifies the organization of data modeling and presentation. In order to be a fast development solution, GOOF provides an automatic code engine by using meta-programming facilities in Java, which could allow users to generate a large amount of routine program codes. Moreover, the pre-built data layer in GOOF connecting with Chado simplifies the process to manage genomic data in the Chado schema. In summary, we studied the way to model genomic data into an informatics framework, a one-stop approach, to organize the data and addressed how GOOF constructs a bioinformatics infrastructure for users to access genomic data

Pervasive computing reference architecture from a software engineering perspective (PervCompRA-SE)

Pervasive computing (PervComp) is one of the most challenging research topics nowadays. Its complexity exceeds the outdated main frame and client-server computation models. Its systems are highly volatile, mobile, and resource-limited ones that stream a lot of data from different sensors. In spite of these challenges, it entails, by default, a lengthy list of desired quality features like context sensitivity, adaptable behavior, concurrency, service omnipresence, and invisibility. Fortunately, the device manufacturers improved the enabling technology, such as sensors, network bandwidth, and batteries to pave the road for pervasive systems with high capabilities. On the other hand, this domain area has gained an enormous amount of attention from researchers ever since it was first introduced in the early 90s of the last century. Yet, they are still classified as visionary systems that are expected to be woven into people’s daily lives. At present, PervComp systems still have no unified architecture, have limited scope of context-sensitivity and adaptability, and many essential quality features are insufficiently addressed in PervComp architectures. The reference architecture (RA) that we called (PervCompRA-SE) in this research, provides solutions for these problems by providing a comprehensive and innovative pair of business and technical architectural reference models. Both models were based on deep analytical activities and were evaluated using different qualitative and quantitative methods. In this thesis we surveyed a wide range of research projects in PervComp in various subdomain areas to specify our methodological approach and identify the quality features in the PervComp domain that are most commonly found in these areas. It presented a novice approach that utilizes theories from sociology, psychology, and process engineering. The thesis analyzed the business and architectural problems in two separate chapters covering the business reference architecture (BRA) and the technical reference architecture (TRA). The solutions for these problems were introduced also in the BRA and TRA chapters. We devised an associated comprehensive ontology with semantic meanings and measurement scales. Both the BRA and TRA were validated throughout the course of research work and evaluated as whole using traceability, benchmark, survey, and simulation methods. The thesis introduces a new reference architecture in the PervComp domain which was developed using a novel requirements engineering method. It also introduces a novel statistical method for tradeoff analysis and conflict resolution between the requirements. The adaptation of the activity theory, human perception theory and process re-engineering methods to develop the BRA and the TRA proved to be very successful. Our approach to reuse the ontological dictionary to monitor the system performance was also innovative. Finally, the thesis evaluation methods represent a role model for researchers on how to use both qualitative and quantitative methods to evaluate a reference architecture. Our results show that the requirements engineering process along with the trade-off analysis were very important to deliver the PervCompRA-SE. We discovered that the invisibility feature, which was one of the envisioned quality features for the PervComp, is demolished and that the qualitative evaluation methods were just as important as the quantitative evaluation methods in order to recognize the overall quality of the RA by machines as well as by human beings