<p>In this thesis we propose a new method for searching for gene products gene products and give annotations associating genes with Gene Ontology codes. Many solutions already exists, using different techniques, however few are capable of addressing the whole GO hierarchy. We propose a method for exploring this hierarchy by dividing it into subtrees, trying to find terms that are characteristics for the subtrees involved. Using a feature selection based on chi-square analysis and naive Bayes classification to find the correct GO nodes.</p>

<p>The research papers about suffix arrays have grown many, and asymptotically better algorithms are being developed. There are, however, two areas that seem to have been a little forgotten - searching in external memory and document retrieval from a suffix array. We present and compare four different methods for document retrieval from an external suffix array. Our results show that only one yields adequate results in the presence of many documents, namely embedding document information into the suffix array. We also touch on the subject of searching external suffix arrays, presenting and discussing four techniques.</p>

<p>Today, more and more applications are web based. As these systems are getting larger and larger, the need for testing them is increasing. XP and other agile methodologies stress the importance of test driven development and automatically testing at all levels of testing. There exists a few open source automatical testing frameworks for web applications' features. These are, however, rather poor when it comes to usability, efficiency and quality factors. This project has created a tool for automatic acceptance testing, called AutAT, which aimes at being an improvement when compared to the previous tools' testing features. The tool has been empirically tested to verify that it is better when it comes to the parameters usability, efficiency and quality. The results from this test clearly show that AutAT is superior to available state of the art open source tools for acceptance testing.</p>

<p>Code reuse in object oriented software development has been common for some time. A recent study performed by the author revealed that while software developers in small Norwegian companies regard code reuse as important and useful, they are prone to perform ad-hoc reuse. This reduces the positive effects achieved through reuse, and although most of the developers wish to perform more systematic reuse, they do not know how to do this. This thesis aims to help amend this problem by developing a set of guidelines describing the process of making a plan for reuse. To develop the guidelines, a literature study was performed, followed by three phases of writing. Between the three phases of writing, two rounds of three feedback interviews were performed to elicit information on the usability and clarity of the guidelines. Each feedback interview was performed with a developer from a small Norwegian company at the developer's workplace. After each set of interviews, the guidelines were revised and improved. The final set of guidelines presented in this report was considered by the developers to be easily understandable and useful, but further work remains to make the guidelines complete; a set of examples of how the process could be performed is essential to help the developers make the leap from the theoretical descriptions of the guidelines to making their own plan for reuse.</p>

<p>This thesis presents a framework of a passively replicated transaction manager. By integrating transactions and replication, two well known fault tolerance techniques, the framework provides high availability for transactional systems and better support for non-deterministic execution for replicated systems. A prototype Java implementation of the framework, based on Jgroup/ARM and Jini, has been developed and performance tests have been executed. The results indicate that the response time for a simple credit-debit transaction heavily depends on the degree of replication for both servers and the transaction manager. E.g. a system with two replicas of the transaction manager and the servers quadruples the response time compared to the nonreplicated case. Thus, the performance penalty of replication should be weighed against the increased availability on a per application basis.</p>

<p>Adaptive systems are systems that react to changes in their environment and adapt to these changes by changing their behavior. The FAMOUS project aims to build an adaptive system by creating a generic middleware platform. This project explores how adaptive systems in general and the FAMOUS project in particular can benefit from using aspect-oriented technology. We propose using run-time aspect weaving to perform adaptations. We create a prototype to demonstrate how one can model aspects for adaptations. We suggest that variability engineering of the applications for an adaptive platform can benefit from aspect-oriented software development.</p>

<p>An observation chart contains a collection of information from several different health information systems used at a hospital. Today, health personnel often has to access these health information systems during patient care and manually register information from them into the observation chart. Integration of the health information systems which constitute an observation chart is therefore needed. Integration means that systems used by a large amount of users are put together in such a way that all users gain access to the information they need. An integration will increase the efficiency of information flow by automatically retrieving information from relevant health information systems into an electronic observation chart. These improvements in turn will hopefully result in better quality of patient care, reduced time spent on treating each patient and therefore also reduced costs. This thesis describes a security focused integration architecture for an electronic observation chart system (EOC-system). This thesis also explores standards, strategies, laws and regulations relevant for the architectural description of the EOC-system. The EOC-system is going to be developed by CARDIAC, a company focusing on technology within health care, and the architectural description will be a support in this development process. The architectural description for CARDIAC’s EOC-system is based on the Model-based Architecture description Framework for Information Integration Abstraction (MAFIIA), which is an architectural description framework for software intensive systems with a specialization towards Information Integration Systems (IIS). The architectural description has also followed MAFIIA’s two extensions, MAFIIA/H and MAFIIA/RBAC, which respectively relate to the health care domain and to role-based access control (RBAC). The work with this thesis, following the MAFIIA architectural description framework, has resulted in a detailed and structured architectural description which sees the architecture from several viewpoints and describes different aspects of it. Security and integration are emphasized in the architectural description; a combination of a service-oriented and portal-oriented integration architecture is chosen and the security mechanisms digital signing, secure communication, auditing and access control are ensured.</p>

<p>Product information exchange has been described by a number of standards. The “Standard for the Exchange of Product model data” (STEP) is published by ISO as an international standard to cover this exchange. “Product Life Cycle Support” (PLCS) is a standard developed as an extension to STEP, covering the complete life cycle information needs for products. PLCS uses Data Exchange Sets (DEXs) to exchange information. A DEX is a subset of the PLCS structure applicable for product information exchange. A DEX is specified in a separate document form the PLCS standard, and is published under OASIS. The development of DEXs is ongoing and changing, nine DEXs have been identified and are being developed within the Organization for the Advancement of Structured Information Standards (OASIS). Each of the nine DEXs covers a specific business concept. Implementations based on the DEX specifications are necessary in order to send and receive populated DEXs with product information. The implementations add contents to a DEX structure in a neutral file format which can be exchanged. Interoperability between senders and receivers of DEXs can not be guaranteed, however, conformance testing of implementations can help increase the chances of interoperability. Conformance testing is the process of testing an implementation against a set of requirements stated in a specification or standard used to develop the implementation. Conformance testing is performed by sending inputs to the implementation and observing the output. The output is then analysed with respect to expected output. STEP dedicates a whole section of the standard to conformance testing of STEP implementations. This section describes how implementations of STEP shall be tested and analysed. PLCS is an extension of STEP, and DEXs are subsets of PLCS. Conformance testing for STEP is used as a basis for DEX conformance testing, because of the similarities between PLCS and STEP. A testing methodology based on STEP conformance testing and DEX specifications is developed. The testing methodology explains how conformance testing can be achieved on DEX implementations exemplified with a test example on a specific DEX. The thesis develops a proposed set of test methods for conformance testing DEX adapter implementations. Conformance testing of Export adapters tests the adapter’s ability to populate and output a correct DEX according to the specifications in the applicable DEX specification. Conformance testing of the Import adapter verifies that the content of the populated input DEX is retrievable in the receiving computer system. A specific DEX, “Identify a part and its constituent parts”, is finally used as an example on how to test a specific DEX specification. Test cases are derived from a set of test requirements identified from the DEX specification. Testing of these requirements is explained explicitly.</p>

<p>With medical imaging, clinicians are given new opportunities in inspection of anatomical structures, surgical planning and diagnosing. Computer vision is often used with the aim of automating these processes. Ultrasound imaging is one of the most popular medical imaging modalities. The equipment is portable and relatively inexpensive, the procedure is non-invasive and there are few known side effects. But the acquisition of ultrasound images, for instance of the heart, is not a trivial job for the inexperienced. Five classes of standard images, or standard views, have been developed to ensure acceptable quality of ultrasound heart images. Automatic recognition of these standard views, or classification, would be a good starting point for an ”Ultrasound for dummies” project. Recently, a new class of object recognition methods has emerged. These methods are based on matching of local features. Image content is transformed into local feature coordinates, which are ideally invariant to translation, rotation, scaling and other image parameters. In [21], David Lowe proposes the Scale Invariant Feature Transform (SIFT), which is a method for extracting distinctive invariant features from an image. He also suggests a method for using these features to recognize different images of the same object. In this thesis I suggest using the SIFT features to classify heart view images. The invariance requirements to a standard heart view recognition system are special. Therefore, in addition to using Lowe’s algorithm for feature extraction, a new matching algorithm specialized at the heart view classification task is proposed.</p>

<p>By distributing the user interface between devices like a PDA and a PC, one can utilize the best characteristic from each device. This thesis has investigated what conceptual models and interface metaphors one should use when designing systems using handheld computers and PCs together. This has been done by exploring the design space of the devices, resulting in seven interface metaphors that have been adapted to a hospital case. Based on results from a focus group session and an interview, several prototypes based on the interface metaphors have been developed. These prototypes all enable a physician to display x-ray images on a patient terminal by using a PDA. In a usability test experiment the users’ actions and think-aloud protocol when using the prototypes have been captured and analyzed to find their mental models. The analysis has resulted in four general metaphors on which users internalize when using handhelds and PCs together. A design process using the user’s mental models as a basis for the creation of the conceptual model is presented. The thesis concludes with that the general metaphors found can be a good basis for the design of a conceptual model and ends with general guidelines for systems using handhelds and PCs together. Keywords: Handheld, PC, conceptual model, mental model, metaphor, design process, usability test, card sort.</p>