CONTEXT: Knowledge is a strategic asset to any organisation due to its usefulness in supporting innovation, performance improvement and competitive advantage. In order to gain the maximum benefit from knowledge, the effective management of various forms of knowledge is increasingly viewed as vital. A Knowledge Management System (KMS) is a class of Information System (IS) that manages organisational knowledge, and KMS software (KMSS) is a KMS component that can be used as a platform for managing various forms of knowledge. The evaluation of the effectiveness or quality of KMS software is challenging, and no systematic evidence exists on the quality evaluation of knowledge management software which considers the various aspects of Knowledge Management (KM) to ensure the effectiveness of a KMS. AIM: The overall aim is to formalise a quality assessment framework for knowledge management software (KMSS). METHOD: In order to achieve the aim, the research was planned and carried out in the stages identified in the software engineering research methods literature. The need for this research was identified through a mapping study of prior KMS research. The data collected through a Systematic Literature Review (SLR) and the evaluation of a KMSS prototype using a sample of 58 regular users of knowledge management software were used as the main sources of data for the formalisation of the quality assessment framework. A test bed for empirical data collection was designed and implemented based on key principles of learning. A formalised quality assessment framework was applied to select knowledge management software and was evaluated for effectiveness. RESULTS: The final outcome of this research is a quality assessment framework consisting of 41 quality attributes categorised under content quality, platform quality and user satisfaction. A Quality Index was formulated by integrating these three categories of quality attributes to evaluate the quality of knowledge management software. CONCLUSION: This research generates novel contributions by presenting a framework for the quality assessment of knowledge management software, never previously available in the research. This framework is a valuable resource for any organisation or individual in selecting the most suitable knowledge management software by considering the quality attributes of the software.

Agile methods are sets of software practices that can produce products faster and at the same time deliver what customers want. Despite these benefits, however, few studies can be found from the Southeast Asia region, particularly Malaysia. Furthermore many of the software processes were developed and produced in the US and European countries so they are tailored to their culture and most empirical evidence come from these countries. In this research, the perception, challenges in relation to Agile adoption and how the methods can be used successfully (the impact/benefits) were investigated from the perspective of Malaysian software practitioners. Consequently the research introduced two models which provide interaction and causality among the factors which can help software practitioners in Malaysia to determine and understand aspects important for successful Agile adoption. Agile focuses on the ‘people aspect’ therefore the cultural differences need to be addressed. Malaysia is a country that has three different ethnicities groups (Malay, Chinese and Indian) and the first language is Malay. English is the second language in the country and it is a standard language used in the business environment including software business. This study started with investigating the awareness of software practitioners in Malaysia regarding Agile methods. Low awareness was identified and interestingly the language aspect and organisational structure/culture were found to have significant association with the awareness of Agile methods. Those using English language were found to be more aware about Agile methods. The adoption of Agile methods in the country seems to be low although this might be changing over time. Issues from the early adopters were qualitatively investigated (with seven organisations and 13 software practitioners) to understand Agile adoption in Malaysia. Customers’education, mind set, people and management were found important from these interviews. The initial results and findings served as background to further investigate factors important in relation to the adoption of Agile methods from the Malaysian perspective. The study continued with a survey and further interviews involving seven organisations (three local and four multinational companies) and 14 software practitioners. While the survey received 207 responses, the language aspect was found significant for Agile usage and the Agile beliefs. Agile usage was also found significant for organisation types (government/non-government), indicating lack of adoption from the government sector. In addition, all factors investigated were found to be significant for getting the impact and benefits of Agile. The strongest relationship was identified from the organisational aspect, followed with the knowledge and involvement from all parties. Qualitative investigation supported and explained the results obtained from the survey and from here, the top factors for adoption and success in applying Agile were discovered to be involvement from all parties which requiring organisation and people to make it happen. The most important factors (or dimensions) identified from both groups (Agile users and non-Agile) were in the dimensions of organisational and people-related aspects (including customers). Finally the study introduced two models which discovered causal relationships in predicting the impact and benefits (success) of Agile methods. This research is based on the empirical investigation; hence the study suggests that Agile methods must be adjusted to the organisation and the people to get involvement from all parties. Agile is more easily adopted in an organisation with low power distance and low uncertainty avoidance. In addition, multinational companies and private sectors were found to facilitate Agile methods. In these organisations, the employees were found to be proficient using English language.

In recent years the software industry has paid significant attention to customising software products by means of outsourcing and Agile development practices. When these areas overlap there are benefits and challenges. This study investigates the customisation process for packaged software products in projects involving multiple clients, and the communication of their requirements across distributed boundaries. A literature review identified the challenges involved and a framework for challenges of customising software products across distributed boundaries (FCCSD) is proposed to address them using onsite development practices. Local decision making and local development are considered as a means of reducing difficulties in communicating the customisation requirements of multiple clients across distributed boundaries through a new model. This model for communicating customisation requirements in the distributed domain, termed (CCRD), has two scenarios, one using decision making at the distributed client’s location, and the second enhancing onsite development of certain requirements in order to reduce delays and misunderstandings between the clients and the teams involved. A preliminary study was conducted to confirm the FCCSD. This employed a questionnaire survey of 19 highly experienced participants. The CCRD model was evaluated in three stages using an industrial case study of a company with 18 distributed clients. The first was a contextual inquiry to create a baseline model for a real world case. The second involved the simulation of the CCRD model using a discrete-event simulation approach, traced by the baseline model using real data. Finally, the findings of previous experiments were validated through a study conducted by means of semi-structured interviews with seven experts at this same company. The key contributions of this study are as follows: First is the proposed framework (FCCSD)that addresses a number of challenges facing customisation across distributed boundaries from literature. Second, this study highlights issues of the communication and negotiation of clients’ customisation requirements across distributed boundaries, and their implications. Therefore, this study demonstrates the statistically significant impact of making decisions and negotiating clients’ requirements, as well as conducting certain development practices, on their premises to limit the implications of communication challenges over distributed boundaries, such as delays in making decisions, a long duration of development and the entire customisation process, and misunderstandings about clients’ requirements.

This thesis is about an empirical study on the effects of using predominant security mechanisms for integration into Agile methodologies. Claims uncovered throughout our review of literature and research are presented along with our findings, analysis, and interpretation of the qualitative and quantitative phases which underscore the gap in the literature in the past few years. In this thesis the researcher uses the issues raised in the literature and incorporates empirical findings from practitioners working in the field to form a cohesive and complete investigation into the predominant security practices that are suitable to be included into Agile. Current security issues related to and applicable to popular Agile methodologies such as Scrum and eXtreme Programming (XP) are examined along with their effects on the process and the final product are researched, quantified, analyzed, interpreted, and summarized. This is done to gain a more practical and in-depth understanding of the security issues and effectiveness of methods proposed for use in the Agile software development field today. The research considered their potential for inclusion (and possible integration) into Agile methods from multiple perspectives utilizing a mixed method approach of in-depth empirical interviews, empirical surveys, and an academic experiment to test those findings. In this manuscript we present the research along with the findings obtained with our conclusions and the future direction of the research. The contribution of this work is to identify and empirically classify outstanding issues that were agreed upon by practitioners and experts in the field. The most popular of these turned out to be the addition of the security engineer or experienced developers to the Agile team to bolster the resulting software’s security assurance argument. Others aimed at modifying aspects of Agile that were deemed necessary for security include documentation, risk analysis, or the need for better tools. Building software with security in mind and the use of software security controls were also important findings from our qualitative phase of the study. This along with our own findings formed the basis of the comprehensive survey of practitioners to gauge the suitability and feasibility of those issues and solutions for possible inclusion into Agile. The significant findings from our survey suggested that the most suitable mechanisms are the addition of a dedicated Security Engineer and the use of more experienced developers to the Agile team, and the use of software security controls. Based on these results we put together an experimental trial to test the effect of more experienced developers on the Agile team on the process, the final product (which is the software produced), and the people involved (which are stakeholders in Agile projects). The statistically significant result of the experiment was in the affirmation of the hypothesis which stated that the inclusion of more experienced developer(s) to the Agile team increased the team’s overall awareness of security compared to the less experienced team(s).

Background: Systematic reviews have become an established methodology in software engineering. However, they are labour intensive, error prone and time consuming. These and other challenges have led to the development of tools to support the process. However, there is limited evidence about their usefulness. Aim: To investigate the usefulness of tools to support systematic reviews in software engineering and develop an evaluation framework for an overall support tool. Method: A literature review, taking the form of a mapping study, was undertaken to identify and classify tools supporting systematic reviews in software engineering. Motivated by its results, a feature analysis was performed to independently compare and evaluate a selection of tools which aimed to support the whole systematic review process. An initial version of an evaluation framework was developed to carry out the feature analysis and later refined based on its results. To obtain a deeper understanding of the technology, a survey was undertaken to explore systematic review tools in other domains. Semi-structured interviews with researchers in healthcare and social science were carried out. Quantitative and qualitative data was collected, analysed and used to further refine the framework. Results: The literature review showed an encouraging growth of tools to support systematic reviews in software engineering, although many had received limited evaluation. The feature analysis provided new insight into the usefulness of tools, determined the strongest and weakest candidate and established the feasibility of an evaluation framework. The survey provided knowledge about tools used in other domains, which helped further refine the framework. Conclusions: Tools to support systematic reviews in software engineering are still immature. Their potential, however, remains high and it is anticipated that the need for tools within the community will increase. The evaluation framework presented aims to support the future development, assessment and selection of appropriate tools.

L'ARN (acide ribonucléique) est une molécule ubiquitaire qui joueplusieurs rôles fondamentaux au sein de la cellule: synthèse desprotéines avec les ARN messagers, activité catalytique ou implicationdans la régulation, les ARN non-codants. Les nouvelles technologies deséquençage à haut- débit permettent de produire des milliards de séquences à moindre coût, posant de manière cruciale la question de l'analyse de ces données.L'objectif de cette thèse est de définir de nouvelles méthodescomputationnelles pour aider à l'analyse de ces séquences dans le casdes ARN non-codants. Dans cette perspective, la "structuresecondaire" d'un ARN, formée par l'ensemble des appariements entrebases, délivre des informations utiles pour étudier la fonction del'ARN. Notre travail se concentre plus particulièrement surl'ensemble des structures potentielles que peut adopter une séquenced'ARN donnée, ensemble que nous appelons "multi-structure". Nousapportons deux contributions: un algorithme pour générersystématiquement toutes les structures localement optimales composantune multi-structure, et un algorithme basé sur la recherche d'unemulti-structure pour identifier un ARN non-codant dans une séquencegénomique. Ces résultats ont été mis en oeuvre dans deux logiciels,Alterna et Regliss, appliqués avec succès à des ensembles de test. / RNA (ribonucleic acid) molecules have various functions in cells. Justas they can store and deliver the DNA message for the proteinsynthesis (messenger RNAs), they can also directly catalyze chemicalreactions or act as a regulator (functional RNAs, also callednon-coding RNAs). Nowadays, recent sequencing technologies yield billions of genomic sequences - DNA, RNA - at a very small cost. However, sequencing isonly the first step: The function of the sequence remains open forinvestigation. The objective of the thesis is to define newcomputational methods to help sequence and structure analysis ofnon-coding RNAs. In this perspective, the "secondary structure" of an RNA,made with base pairs, provides useful hints to further study itsfunction. Our work is focused on sets of all possible RNA structuresfor a given sequence, introducing the concept of "RNAmulti-structures". The thesis details how such sets can be constructed systematically to generate all locally optimal secondary structures, and how they can be used as a pattern to identify non-coding RNAs in genomic sequences.We provide efficient algorithms for these two problems. Thesealgorithms have been implementated in the software tools Alterna andRegliss and tested on real data, providing new insight into RNAstructures.

Aspect-Oriented Software Development provides a means to modularize concerns of a system which are scattered over multiple system modules. These concerns are known as crosscutting concerns and they cause code to be scattered and tangled in multiple system units. The technique was first proposed at the programming level but evolved up through to the other phases of the software development lifecycle with the passage of time. At the moment, aspect-orientation is addressed in all phases of software development, such as requirements engineering, architecture, design and implementation. This thesis focuses on aspect oriented software design and provides a design language, Aspect-Oriented Design Language (AODL), to specify, represent and design aspectual constructs. The language has been designed to implement co-designing of aspectual and non aspectual constructs. The obliviousness between the constructs has been minimized to improve comprehensibility of the models. The language is applied in three phases and for each phase a separate set of design notations has been introduced. The design notations and diagrams are extensions of Unified Modelling Language (UML) and follow UML Meta Object Facility (UML MOF) rules. There is a separate notation for each aspectual construct and a set of design diagrams to represent their structural and behavioural characteristics. In the first phase, join points are identified and represented in the base program. A distinct design notation has been designated for join points, through which they are located using two diagrams, Join Point Identification Diagram and Join Point Behavioural Diagram. The former diagram identifies join points in a structural depiction of message passing among objects and the later locates them during the behavioural flow of activities of the system. In the second phase, aspects are designed using an Aspect Design Model that models the structural representation of an aspect. The model contains the aspect‟s elements and associations among them. A special diagram, known as the pointcut advice diagram, is nested in the model to represent relationship between pointcuts and their related advices. The rest of the features, such as attributes, operations and inter-type declarations are statically represented in the model. In the third and the final phase, composition of aspects is designed. There are three diagrams included in this phase. To design dynamic composition of aspects with base classes, an Aspect-Class Dynamic Model has been introduced. It depicts the weaving of advices into the base program during the execution of the system. The structural representation of this weaving is modelled using Aspect-Class Structural Model, which represents the relationships between aspects and base classes. The third model is the Pointcut Composition Model, which is a fine-grained version of the Aspect-Class Dynamic Model and has been proposed to depict a detailed model of compositions at pointcut-level. Besides these models, a tabular specification of pointcuts has also been introduced that helps in documenting pointcuts along with their parent aspects and interacting classes. AODL has been evaluated in two stages. In the first stage, two detailed case studies have been modelled using AODL. The first case study is an unimplemented system that is forward designed using AODL notations and diagrams, and the second is an implemented system which is reverse engineered and designed in AODL. A qualitative evaluation has been conducted in the second stage of evaluation to assess the efficacy and maturity of the language. The evaluation also compares the language with peer modelling approaches.

The rapid development of key mobile technology supporting the ‘Internet of Things’, such as 3G, Radio Frequency Identification (RFID), and Zigbee etc. and the advanced decision making methods have improved the Decision-Making System (DMS) significantly in the last decade. Advanced wireless technology can provide a real-time data collection to support DMS and the effective decision making techniques based on the real-time data can improve Supply Chain (SC) efficiency. However, it is difficult for Small and Medium sized Enterprises (SMEs) to effectively adopt this technology because of the complexity of technology and methods, and the limited resources of SMEs. Consequently, a suitable DMS which can support effective decision making is required in the operation of SMEs in SCs. This thesis conducts research on developing an adaptive simulation-based DMS for SMEs in the manufacturing sector. This research is to help and support SMEs to improve their competitiveness by reducing costs, and reacting responsively, rapidly and effectively to the demands of customers. An adaptive developed framework is able to answer flexible ‘what-if’ questions by finding, optimising and comparing solutions under the different scenarios for supporting SME-managers to make efficient and effective decisions and more customer-driven enterprises. The proposed framework consists of simulation blocks separated by data filter and convert layers. A simulation block may include cell simulators, optimisation blocks, and databases. A cell simulator is able to provide an initial solution under a special scenario. An optimisation block is able to output a group of optimum solutions based on the initial solution for decision makers. A two-phase optimisation algorithm integrated Conflicted Key Points Optimisation (CKPO) and Dispatching Optimisation Algorithm (DOA) is proposed for the condition of Jm|STsi,b with Lot-Streaming (LS). The feature of the integrated optimisation algorithm is demonstrated using a UK-based manufacture case study. Each simulation block is a relatively independent unit separated by the relevant data layers. Thus SMEs are able to design their simulation blocks according to their requirements and constraints, such as small budgets, limited professional staff, etc. A simulation block can communicate to the relative simulation block by the relevant data filter and convert layers and this constructs a communication and information network to support DMSs of Supply Chains (SCs). Two case studies have been conducted to validate the proposed simulation framework. An SME which produces gifts in a SC is adopted to validate the Make To Stock (MTS) production strategy by a developed stock-driven simulation-based DMS. A schedule-driven simulation-based DMS is implemented for a UK-based manufacturing case study using the Make To Order (MTO) production strategy. The two simulation-based DMSs are able to provide various data to support management decision making depending on different scenarios.

Les développeurs occupent une place prépondérante dans le développement logiciel. Dans ce cadre, ils doivent réaliser une succession de tâches élémentaires (analyse, codage, liaison avec le code existant...), mais pour effectuer ces tâches, un développeur doit régulièrement changer de contexte de travail (recherche d’information, lecture de code…) et analyser du code qui n’est pas le sien. Ces actions nécessitent un temps d’adaptation élevé et réduisent l’efficacité du développeur. La modélisation logicielle est une solution à ce type de problème. Elle propose une vue abstraite d’un logiciel, des liens entre ses entités ainsi que des algorithmes utilisés. Cependant, l’Ingénierie Dirigée par les Modèles (IDM) est encore trop peu utilisée en entreprise. Dans cette thèse, nous proposons un outil pour améliorer la compréhension d’un programme à l’aide de diagrammes dynamiques et interactifs. Cet outil se nomme VisUML et est centré sur l’activité principale de codage du développeur. VisUML fournit des vues (sur des pages web ou sur des outils de modélisation) synchronisées avec le code. Les diagrammes UML générés sont interactifs et permettent une navigation rapide avec et dans le code. Cette navigation réduit les pertes de temps et de contextes dues aux changements d’activités en fournissant à tout moment une vue abstraite sous forme de diagramme des éléments actuellement ouverts dans l’outil de codage du développeur. Au final, VisUML a été évalué par vingt développeurs dans le cadre d’une expérimentation qualitative de l’outil afin d’estimer l’utilité d’un tel outil. / Developers dominate in software development. In this context, they must perform a succession of elementary tasks (analysis, coding, linking with existing code ...), but in order to perform these tasks, a developer must regularly change his context of work (search information, read code ...) and analyze code that is not his. These actions require a high adaptation time and reduce the efficiency of the developer. Software modeling is a solution to this type of problem. It offers an abstract view of a software, links between its entities as well as algorithms used. However, Model-Driven Engineering (MDE) is still underutilized in business. In this thesis, we propose a tool to improve the understanding of a program using dynamic and interactive diagrams. This tool is called VisUML and focuses on the main coding activity of the developer. VisUML provides views (on web pages or modeling tools) synchronized with the code.The generated UML diagrams are interactive and allow fast navigation with and in the code. This navigation reduces the loss of time and context due to activity changes by providing at any time an abstract diagram view of the elements currently open in the developer’s coding tool. In the end, VisUML was evaluated by twenty developers as part of a qualitative experimentation of the tool to estimate the usefulness of such a tool.

No matter which tools, techniques, and methodologies are used for software development, it remains an error-prone process. Nevertheless, changing such important constituents of the software process surely has an effect on the types of faults inherent in the developed software. For instance, some types of faults are typical for structured development, whereas others are typical for object-oriented development. This chapter explores the question of whether component-based software requires new testing techniques, and proposes an integrated testing technique. This technique integrates various tasks during testing component-based software: whiteand black-box testing of the main component (i.e., the top level component controlling the other components), black-box testing of components, black-box testing of the middleware and integration testing of the main component with other components. Benefits of this technique are shown using a real-world example: the technique is automatable and applicable to existing component-based software.