Overcoming the Complexity of Software Product Management

This thesis describes an approach to overcoming the complexity of software product management (SPM) and consists of several studies that investigate the activities and roles in product management, as well as issues related to the adoption of software product management. The thesis focuses on organizations that have started the adoption of SPM but faced difficulties due to its complexity and fuzziness and suggests the frameworks for overcoming these challenges using the principles of decomposition and iterative improvements. The research process consisted of three phases, each of which provided complementary results and empirical observation to the problem of overcoming the complexity of SPM. Overall, product management processes and practices in 13 companies were studied and analysed. Moreover, additional data was collected with a survey conducted worldwide. The collected data were analysed using the grounded theory (GT) to identify the possible ways to overcome the complexity of SPM. Complementary research methods, like elements of the Theory of Constraints were used for deeper data analysis. The results of the thesis indicate that the decomposition of SPM activities depending on the specific characteristics of companies and roles is a useful approach for simplifying the existing SPM frameworks. Companies would benefit from the results by adopting SPM activities more efficiently and effectively and spending fewer resources on its adoption by concentrating on the most important SPM activities.

Scaling up stepwise feature introduction to construction of large software systems

Developing software is a difficult and error-prone activity. Furthermore, the complexity of modern computer applications is significant. Hence,an organised approach to software construction is crucial. Stepwise Feature Introduction – created by R.-J. Back – is a development paradigm, in which software is constructed by adding functionality in small increments. The resulting code has an organised, layered structure and can be easily reused. Moreover, the interaction with the users of the software and the correctness concerns are essential elements of the development process, contributing to high quality and functionality of the final product. The paradigm of Stepwise Feature Introduction has been successfully applied in an academic environment, to a number of small-scale developments. The thesis examines the paradigm and its suitability to construction of large and complex software systems by focusing on the development of two software systems of significant complexity. Throughout the thesis we propose a number of improvements and modifications that should be applied to the paradigm when developing or reengineering large and complex software systems. The discussion in the thesis covers various aspects of software development that relate to Stepwise Feature Introduction. More specifically, we evaluate the paradigm based on the common practices of object-oriented programming and design and agile development methodologies. We also outline the strategy to testing systems built with the paradigm of Stepwise Feature Introduction.

Using Moodle to provide added value in the teaching of a software development course

The rate of adoption and use of learning management systems to support teaching and learning processes in academic institutions is growing rapidly. Universities are acquiring systems with functionalities that can match with their specific needs and requirements. Moodle is one of the most popular and widely deployed learning management systems in academic institutions today. However, apart from the system, universities tend to maintain other applications for the purpose of supplementing their teaching and learning processes. This situation is similar to Lappeenranta University of Technology (LUT), which is our case study in this project. Apart from Moodle, the university also maintains other systems such as Oodi, Noppa and Uni portal for the purpose of supporting its educational activities. This thesis has two main goals. The first goal is to understand the specific role of Moodle at LUT. This information is fundamental in assessing whether Moodle is needed in the university’s current teaching and learning environment. The second aim is to provide insights to teachers and other departmental stakeholders on how Moodle can provide added value in the teaching of a software development course. In response to this, a Moodle module for a software development course is created and the underlying features are tested. Results of the constructive work proposed some improvements through (i) the use of Moodle for in-class surveys, (ii) transfer of grades from Moodle to Oodi, (iii) use of Moodle in self-study courses and MOOCs, (iv) online examinations, and (v) Moodle integrations with third party applications. The proposed items were then evaluated for their utility through interviews of five expert interviews. The final results of this work are considered useful to LUT administration and management specifically on ways that Moodle can bring changes to the university at managerial, economical and technical level. It also poses some challenges on platform innovations and research.

ANATI QUANTI: software de análises quantitativas para estudos em anatomia vegetal

Em diversos estudos interdisciplinares em que a Anatomia Vegetal é utilizada, análises quantitativas complementares são necessárias. Geralmente, a avaliação micromorfométrica é feita manualmente e/ou utilizando programas computacionais de análise de imagens não específicos. Este trabalho teve como objetivo desenvolver um programa específico para Anatomia Vegetal quantitativa e testar sua eficiência e aceitação por usuários. A solução foi elaborada na linguagem Java, visando maior mobilidade em relação ao sistema operacional a ser usado. O software desenvolvido foi denominado ANATI QUANTI e testado pelos alunos, pesquisadores e professores do Laboratório de Anatomia Vegetal da Universidade Federal de Viçosa (UFV). Todos os entrevistados receberam fotos para efetuarem medições no ANATI QUANTI e comparar com os resultados obtidos utilizando o software disponível. Os voluntários, através de questionários previamente formulados, destacaram as principais vantagens e desvantagens do programa desenvolvido em relação ao software disponível. Além de ser mais específico, simples e ágil do que o software disponível, o ANATI QUANTI é confiável, atendendo à expectativa dos entrevistados. Entretanto, há necessidade de acrescentar recursos adicionais, como a inserção de novas escalas, o que aumentaria a gama de usuários. O ANATI QUANTI já está em uso nas pesquisas desenvolvidas por usuários na UFV. Por ser um software livre e de código aberto, será disponibilizado na internet gratuitamente.

Transcriptional and Epigenetic Regulation of Human CD4+ T Helper Lineage Specification

Activated T helper (Th) cells have ability to differentiate into functionally distinct Th1, Th2 and Th17 subsets through a series of overlapping networks that include signaling and transcriptional control and the epigenetic mechanisms to direct immune responses. However, inappropriate execution in the differentiation process and abnormal function of these Th cells can lead to the development of several immune mediated diseases. Therefore, the thesis aimed at identifying genes and gene regulatory mechanisms responsible for Th17 differentiation and to study epigenetic changes associated with early stage of Th1/Th2 cell differentiation. Genome wide transcriptional profiling during early stages of human Th17 cell differentiation demonstrated differential regulation of several novel and currently known genes associated with Th17 differentiation. Selected candidate genes were further validated at protein level and their specificity for Th17 as compared to other T helper subsets was analyzed. Moreover, combination of RNA interference-mediated downregulation of gene expression, genome-wide transcriptome profiling and chromatin immunoprecipitation followed by massive parallel sequencing (ChIP-seq), combined with computational data integration lead to the identification of direct and indirect target genes of STAT3, which is a pivotal upstream transcription factor for Th17 cell polarization. Results indicated that STAT3 directly regulates the expression of several genes that are known to play a role in activation, differentiation, proliferation, and survival of Th17 cells. These results provide a basis for constructing a network regulating gene expression during early human Th17 differentiation. Th1 and Th2 lineage specific enhancers were identified from genome-wide maps of histone modifications generated from the cells differentiating towards Th1 and Th2 lineages at 72h. Further analysis of lineage-specific enhancers revealed known and novel transcription factors that potentially control lineage-specific gene expression. Finally, we found an overlap of a subset of enhancers with SNPs associated with autoimmune diseases through GWASs suggesting a potential role for enhancer elements in the disease development. In conclusion, the results obtained have extended our knowledge of Th differentiation and provided new mechanistic insights into dysregulation of Th cell differentiation in human immune mediated diseases.

Design and validation of stateful composite RESTful web services

A web service is a software system that provides a machine-processable interface to the other machines over the network using different Internet protocols. They are being increasingly used in the industry in order to automate different tasks and offer services to a wider audience. The REST architectural style aims at producing scalable and extensible web services using technologies that play well with the existing tools and infrastructure of the web. It provides a uniform set of operation that can be used to invoke a CRUD interface (create, retrieve, update and delete) of a web service. The stateless behavior of the service interface requires that every request to a resource is independent of the previous ones facilitating scalability. Automated systems, e.g., hotel reservation systems, provide advanced scenarios for stateful services that require a certain sequence of requests that must be followed in order to fulfill the service goals. Designing and developing such services for advanced scenarios with REST constraints require rigorous approaches that are capable of creating web services that can be trusted for their behavior. Systems that can be trusted for their behavior can be termed as dependable systems. This thesis presents an integrated design, analysis and validation approach that facilitates the service developer to create dependable and stateful REST web services. The main contribution of this thesis is that we provide a novel model-driven methodology to design behavioral REST web service interfaces and their compositions. The behavioral interfaces provide information on what methods can be invoked on a service and the pre- and post-conditions of these methods. The methodology uses Unified Modeling Language (UML), as the modeling language, which has a wide user base and has mature tools that are continuously evolving. We have used UML class diagram and UML state machine diagram with additional design constraints to provide resource and behavioral models, respectively, for designing REST web service interfaces. These service design models serve as a specification document and the information presented in them have manifold applications. The service design models also contain information about the time and domain requirements of the service that can help in requirement traceability which is an important part of our approach. Requirement traceability helps in capturing faults in the design models and other elements of software development environment by tracing back and forth the unfulfilled requirements of the service. The information about service actors is also included in the design models which is required for authenticating the service requests by authorized actors since not all types of users have access to all the resources. In addition, following our design approach, the service developer can ensure that the designed web service interfaces will be REST compliant. The second contribution of this thesis is consistency analysis of the behavioral REST interfaces. To overcome the inconsistency problem and design errors in our service models, we have used semantic technologies. The REST interfaces are represented in web ontology language, OWL2, that can be part of the semantic web. These interfaces are used with OWL 2 reasoners to check unsatisfiable concepts which result in implementations that fail. This work is fully automated thanks to the implemented translation tool and the existing OWL 2 reasoners. The third contribution of this thesis is the verification and validation of REST web services. We have used model checking techniques with UPPAAL model checker for this purpose. The timed automata of UML based service design models are generated with our transformation tool that are verified for their basic characteristics like deadlock freedom, liveness, reachability and safety. The implementation of a web service is tested using a black-box testing approach. Test cases are generated from the UPPAAL timed automata and using the online testing tool, UPPAAL TRON, the service implementation is validated at runtime against its specifications. Requirement traceability is also addressed in our validation approach with which we can see what service goals are met and trace back the unfulfilled service goals to detect the faults in the design models. A final contribution of the thesis is an implementation of behavioral REST interfaces and service monitors from the service design models. The partial code generation tool creates code skeletons of REST web services with method pre and post-conditions. The preconditions of methods constrain the user to invoke the stateful REST service under the right conditions and the post condition constraint the service developer to implement the right functionality. The details of the methods can be manually inserted by the developer as required. We do not target complete automation because we focus only on the interface aspects of the web service. The applicability of the approach is demonstrated with a pedagogical example of a hotel room booking service and a relatively complex worked example of holiday booking service taken from the industrial context. The former example presents a simple explanation of the approach and the later worked example shows how stateful and timed web services offering complex scenarios and involving other web services can be constructed using our approach.

Cost-benefit analysis of using test automation in the development of embedded software

The goal of this thesis is to make a case study of test automation’s profitability in the development of embedded software in a real industrial setting. The cost-benefit analysis is done by considering the costs and benefits test automation causes to software development, before the software is released to customers. The potential benefits of test automation regarding software quality after customer release were not estimated. Test automation is a significant investment which often requires dedicated resources. When done accordingly, the investment in test automation can produce major cost savings by reducing the need for manual testing effort, especially if the software is developed with an agile development framework. It can reduce the cost of avoidable rework of software development, as test automation enables the detection of construction time defects in the earliest possible moment. Test automation also has many pitfalls such as test maintainability and testability of the software, and if those areas are neglected, the investment in test automation may become worthless or it may even produce negative results. The results of this thesis suggest that test automation is very profitable at the company under study.

Challenges in managing large-scale agile software development transformation

Adapting and scaling up agile concepts, which are characterized by iterative, self-directed, customer value focused methods, may not be a simple endeavor. This thesis concentrates on studying challenges in a large-scale agile software development transformation in order to enhance understanding and bring insight into the underlying factors for such emerging challenges. This topic is approached through understanding the concepts of agility and different methods compared to traditional plan-driven processes, complex adaptive theory and the impact of organizational culture on agile transformational efforts. The empirical part was conducted by a qualitative case study approach. The internationally operating software development case organization had a year of experience of an agile transformation effort during it had also undergone organizational realignment efforts. The primary data collection was conducted through semi-structured interviews supported by participatory observation. As a result the identified challenges were categorized under four broad themes: organizational, management, team dynamics and process related. The identified challenges indicate that agility is a multifaceted concept. Agile practices may bring visibility in issues of which many are embedded in the organizational culture or in the management style. Viewing software development as a complex adaptive system could facilitate understanding of the underpinning philosophy and eventually solving the issues: interactions are more important than processes and solving a complex problem, such a novel software development, requires constant feedback and adaptation to changing requirements. Furthermore, an agile implementation seems to be unique in nature, and agents engaged in the interaction are the pivotal part of the success of achieving agility. In case agility is not a strategic choice for whole organization, it seems additional issues may arise due to different ways of working in different parts of an organization. Lastly, detailed suggestions to mitigate the challenges of the case organization are provided.

Developing Bioimage Informatics – from Microscopy to Software Solutions – with alpha2beta1 Integrin as a Case Study

Biokuvainformatiikan kehittäminen – mikroskopiasta ohjelmistoratkaisuihin – sovellusesimerkkinä α2β1-integriini Kun ihmisen genomi saatiin sekvensoitua vuonna 2003, biotieteiden päätehtäväksi tuli selvittää eri geenien tehtävät, ja erilaisista biokuvantamistekniikoista tuli keskeisiä tutkimusmenetelmiä. Teknologiset kehitysaskeleet johtivat erityisesti fluoresenssipohjaisten valomikroskopiatekniikoiden suosion räjähdysmäiseen kasvuun, mutta mikroskopian tuli muuntua kvalitatiivisesta tieteestä kvantitatiiviseksi. Tämä muutos synnytti uuden tieteenalan, biokuvainformatiikan, jonka on sanottu mahdollisesti mullistavan biotieteet. Tämä väitöskirja esittelee laajan, poikkitieteellisen työkokonaisuuden biokuvainformatiikan alalta. Väitöskirjan ensimmäinen tavoite oli kehittää protokollia elävien solujen neliulotteiseen konfokaalimikroskopiaan, joka oli yksi nopeimmin kasvavista biokuvantamismenetelmistä. Ihmisen kollageenireseptori α2β1-integriini, joka on tärkeä molekyyli monissa fysiologisissa ja patologisissa prosesseissa, oli sovellusesimerkkinä. Työssä saavutettiin selkeitä visualisointeja integriinien liikkeistä, yhteenkeräytymisestä ja solun sisään siirtymisestä, mutta työkaluja kuvainformaation kvantitatiiviseen analysointiin ei ollut. Väitöskirjan toiseksi tavoitteeksi tulikin tällaiseen analysointiin soveltuvan tietokoneohjelmiston kehittäminen. Samaan aikaan syntyi biokuvainformatiikka, ja kipeimmin uudella alalla kaivattiin erikoistuneita tietokoneohjelmistoja. Tämän väitöskirjatyön tärkeimmäksi tulokseksi muodostui näin ollen BioImageXD, uudenlainen avoimen lähdekoodin ohjelmisto moniulotteisten biokuvien visualisointiin, prosessointiin ja analysointiin. BioImageXD kasvoi yhdeksi alansa suurimmista ja monipuolisimmista. Se julkaistiin Nature Methods -lehden biokuvainformatiikkaa käsittelevässä erikoisnumerossa, ja siitä tuli tunnettu ja laajalti käytetty. Väitöskirjan kolmas tavoite oli soveltaa kehitettyjä menetelmiä johonkin käytännönläheisempään. Tehtiin keinotekoisia piidioksidinanopartikkeleita, joissa oli "osoitelappuina" α2β1-integriinin tunnistavia vasta-aineita. BioImageXD:n avulla osoitettiin, että nanopartikkeleilla on potentiaalia lääkkeiden täsmäohjaussovelluksissa. Tämän väitöskirjatyön yksi perimmäinen tavoite oli edistää uutta ja tuntematonta biokuvainformatiikan tieteenalaa, ja tämä tavoite saavutettiin erityisesti BioImageXD:n ja sen lukuisten julkaistujen sovellusten kautta. Väitöskirjatyöllä on merkittävää potentiaalia tulevaisuudessa, mutta biokuvainformatiikalla on vakavia haasteita. Ala on liian monimutkainen keskimääräisen biolääketieteen tutkijan hallittavaksi, ja alan keskeisin elementti, avoimen lähdekoodin ohjelmistokehitystyö, on aliarvostettu. Näihin seikkoihin tarvitaan useita parannuksia,

Building Successful, Open Repository Software Ecosystems: Technology and Community

Panel at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Analyses of the usefulness of Software Defined Storage Solutions for Web-based Digital Preservation Applications

Presentation at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Software and Code Finder: making research outputs visible

Poster at Open Repositories 2014, Helsinki, Finland, June 9-13, 2014

Software product line for power converters

Työn tilaajana toimi Visedo Oy. Työn tavoitteina oli tutkia Visedo Oy:n ohjelmistokehityksen nykytila, tunnistaa seuraavat parannuskohteet ja antaa ohjeita havaittujen parannuskohteiden korjaamiseksi. Visedo Oy:n tehonmuokkain ohjelmistokehityksen nykytilaa käsiteltiin neljän valitun osa-alueen näkökulmasta: ohjelmistoarkkitehtuurityyli, komponenttipohjainen ohjelmistokehitys, ohjelmistotuotelinjojen kehitysmenetelmät ja ohjelmistovariaatioiden hallinta. Valituilla osa-alueilla havaittujen parannuskohteiden perusteella annettiin korjausehdotuksia: ohjelmistoarkkitehtuurin rakenteeseen, komponenttien jakautumiselle, komponenttien koostamiselle ja komponenttien versioinnille. Lisäksi ehdotettiin uudenlaista ohjelmistotuotelinja rakennetta, joka yhdistää kerros- ja komponenttipohjaiset arkkitehtuurityylit mahdollistaen ominaisuuksiltaan eroavien tehonmuokkain ohjelmistojen hallinnan.