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,

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.

Comparison of Different Concentrated Solar Power Collector Designs and Development of a Linear Fresnel Solar Collector Model

Concentrated solar power (CSP) is a renewable energy technology, which could contribute to overcoming global problems related to pollution emissions and increasing energy demand. CSP utilizes solar irradiation, which is a variable source of energy. In order to utilize CSP technology in energy production and reliably operate a solar field including thermal energy storage system, dynamic simulation tools are needed in order to study the dynamics of the solar field, to optimize production and develop control systems. The object of this Master’s Thesis is to compare different concentrated solar power technologies and configure a dynamic solar field model of one selected CSP field design in the dynamic simulation program Apros, owned by VTT and Fortum. The configured model is based on German Novatec Solar’s linear Fresnel reflector design. Solar collector components including dimensions and performance calculation were developed, as well as a simple solar field control system. The preliminary simulation results of two simulation cases under clear sky conditions were good; the desired and stable superheated steam conditions were maintained in both cases, while, as expected, the amount of steam produced was reduced in the case having lower irradiation conditions. As a result of the model development process, it can be concluded, that the configured model is working successfully and that Apros is a very capable and flexible tool for configuring new solar field models and control systems and simulating solar field dynamic behaviour.

Customer-driven service product development

This thesis studies customer-driven service product development and how to manage customer involvement in the service product development process. The theory part of this thesis is a literature review of the prior studies and the thesis also includes empirical evidence in the form of a case study about ABB.

A systematic mapping study on technical debt definition

The goal of this study was to explore and understand the definition of technical debt. Technical debt refers to situation in a software development, where shortcuts or workarounds are taken in technical decision. However, the original definition has been applied to other parts of software development and it is currently difficult to define technical debt. We used mapping study process as a research methodology to collect literature related to the research topic. We collected 159 papers that referred to original definition of technical debt, which were retrieved from scientific literature databases to conduct the search process. We retrieved 107 definitions that were split into keywords. The keyword map is one of the main results of this work. Apart from that, resulting synonyms and different types of technical debt were analyzed and added to the map as branches. Overall, 33 keywords or phrases, 6 synonyms and 17 types of technical debt were distinguished.

Identification of characteristics for successful university-company partnership development

The importance of university-company collaboration has increased during the last decades. The drivers for that are, on the one hand, changes in business logic of companies and on the other hand the decreased state funding of universities. Many companies emphasize joint research with universities as an enabling input to their development processes, which aim at creating new innovations, products and wealth. These factors have changed universities’ operations and they have adopted several practices of dynamic business organizations, such as strategic planning, monitoring and controlling methods of internal processes etc. The objective of this thesis is to combine different characteristics of successful university-company partnership and its development. The development process starts with identifying potential partners in the university’s interest group, which requires understanding the role of different partners in the innovation system. Next, in order to find a common development basis, matching the policy and strategy between partners is needed. The third phase is to combine the academic and industrial objectives of a joint project, which is a typical form of university-company collaboration. The optimum is a win-win situation where both partners, universities and companies, can get addedvalue. For the companies added value typically means access to new research results before their competitors. For the universities added value offers a possibility to carry on high level scientific work. The research output in the form of published scientific articles is evaluated by the international science community. Because the university-company partnership is often executed by joint projects, the different forms of this kind of projects is discussed in this study. The most challenging form of collaboration is a semi-open project model, which is not based on bilateral activities between universities and companies but on a consortium of several universities, research institutes and companies. The universities and companies are core actors in the innovation system. Thus the discussion of their roles and relations to public operators like publicly funded financiers is important. In the Finnish innovation system there are at least the following doers executing strategies and policies: EU, Academy of Finland and TEKES. In addition to these, Strategic Centres for Science, Technology and Innovation which are owned jointly by companies, universities and research organizations have a very important role in their fields of business. They transfer research results into commercial actions to generate wealth. The thesis comprises two parts. The first part consists of an overview of the study including introduction, literature review, research design, synthesis of findings and conclusions. The second part introduces four original research publications.

User Experience of Geocaching and Its Application to Tourism and Education

Advances in technology have provided new ways of using entertainment and game technology to foster human interaction. Games and playing with games have always been an important part of people’s everyday lives. Traditionally, human-computer interaction (HCI) research was seen as a psychological cognitive science focused on human factors, with engineering sciences as the computer science part of it. Although cognitive science has made significant progress over the past decade, the influence of people’s emotions on design networks is increasingly important, especially when the primary goal is to challenge and entertain users (Norman 2002). Game developers have explored the key issues in game design and identified that the driving force in the success of games is user experience. User-centered design integrates knowledge of users’ activity practices, needs, and preferences into the design process. Geocaching is a location-based treasure hunt game created by a community of players. Players use GPS (Global Position System) technology to find “treasures” and create their own geocaches; the game can be developed when the players invent caches and used more imagination to creations the caches. This doctoral dissertation explores user experience of geocaching and its applications in tourism and education. Globally, based on the Geocaching.com webpage, geocaching has been played about 180 countries and there are more than 10 million registered geocachers worldwide (Geocaching.com, 25.11.2014). This dissertation develops and presents an interaction model called the GameFlow Experience model that can be used to support the design of treasure hunt applications in tourism and education contexts. The GameFlow Model presents and clarifies various experiences; it provides such experiences in a real-life context, offers desirable design targets to be utilized in service design, and offers a perspective to consider when evaluating the success of adventure game concepts. User-centered game designs have adapted to human factor research in mainstream computing science. For many years, the user-centered design approach has been the most important research field in software development. Research has been focusing on user-centered design in software development such as office programs, but the same ideas and theories that will reflect the needs of a user-centered research are now also being applied to game design (Charles et al. 2005.) For several years, we have seen a growing interest in user experience design. Digital games are experience providers, and game developers need tools to better understand the user experience related to products and services they have created. This thesis aims to present what the user experience is in geocaching and treasure hunt games and how it can be used to develop new concepts for the treasure hunt. Engineers, designers, and researchers should have a clear understanding of what user experience is, what its parts are, and most importantly, how we can influence user satisfaction. In addition, we need to understand how users interact with electronic products and people, and how different elements synergize their experiences. This doctoral dissertation represents pioneering work on the user experience of geocaching and treasure hunt games in the context of tourism and education. The research also provides a model for game developers who are planning treasure hunt concepts.

Ohjelmistotestauksen käytänteet Suomessa

Ohjelmistotestauksen merkitys on kasvanut sen mukaan mitä enemmän ohjelmisto-tuotteet vaikuttavat jokapäiväisesseen elämämme. Tämän vuoksi yritysten investointien ja laadunvarmentamisen yhteys on ilmeinen. Organisaatiot panostavat yhä enemmän ei–funktionaaliseen testaukseen, kuten turvallisuuden, suorituskyvyn ja käytettävyyden testaamiseen. Tämän työn tarkoituksena on tutkia ohjelmistotestauksen nykytilannetta Suomessa. Syy tähän on uudistaa ja parantaa ohjelmistotestauksen kurssitarjontaa Turun yliopistossa vastaamaan parhaalla mahdollisella tavalla yritysten tarvetta. Opinnäyte on toteutettu replikaatio-tutkimuksena. Pääosa kyselystä sisältää kysymyksiä ohjelmistotestauksen menetelmistä ja työkaluista testausprosessin toimintojen aikana. Lisäksi on yleisiä kysymyksiä yrityksistä ja niiden ohjelmistotestausympäristöistä. Kyselyssä otetaan myös kantaa yritysten käyttämiin monenlaisiin testaus-tasoihin, -tyyppeihin ja testauksessa kohdattuihin haasteisiin. Tämä opinnäyte perustuu testausprosessistandardeihin. Ohjelmistotestausstandardit ovat keskeisessä asemassa tässä työssä, vaikka ne ovat olleet viime aikoina vahvan kritiikin kohteena. Epäilys standardien välttämättömyyteen on syntynyt muutoksista ohjelmistokehityksessä. Tämä työ esittelee tulokset ohjelmistotestauksen käytännöistä. Tuloksia on verrattu aiheeseen liittyvän aiemman kyselyn (Lee, Kang, & Lee, 2011) tuloksiin. Ajanpuutteen havaitaan olevan suuri haaste ohjelmistotestauksessa. Ketterä ohjelmistokehitys on saavuttanut suosiota kaikissa vastaajien yrityksissä. Testauksen menetelmät ja työkalut testauksen arviointiin, suunnitteluun ja raportointiin ovat hyvin vähäisessä käytössä. Toisaalta testauksen menetelmien ja työkalujen käyttö automaattiseen testauksen toteuttamiseen ja virheiden hallintaan on lisääntynyt. Järjestelmä-, hyväksyntä-, yksikkö- ja integraatiotestaus ovat käytössä kaikkien vastaajien edustamissa yrityksissä. Kaikkien vastaajien mielestä regressio- sekä tutkiva- ja ei-funktionaalinen testaus ovat tärkeitä tekniikoita.

Product Assurance in Agile Space Systems Development

Product assurance is an essential part of product development process if developers want to ensure that final product is safe and reliable. Product assurance can be supported withrisk management and with different failure analysis methods. Product assurance is emphasized in system development process of mission critical systems. The product assurance process in systems of this kind requires extra attention. Inthis thesis, mission critical systems are space systems and the product assurance processof these systems is presented with help of space standards. The product assurance process can be supported with agile development because agile emphasizes transparency of the process and fast response to changes. Even if the development process of space systems is highly standardized and reminds waterfall model, it is still possible to adapt agile development in space systems development. This thesisaims to support the product assurance process of space systems with agile developmentso that the final product would be as safe and reliable as possible. The main purpose of this thesis is to examine how well product assurance is performed in Finnish space organizations and how product assurance tasks and activities can besupported with agile development. The research part of this thesis is performed in survey form.

Product assurance in agile space systems development

Product assurance is an essential part of product development process if developers want to ensure that final product is safe and reliable. Product assurance can be supported with risk management and with different failure analysis methods. Product assurance is emphasized in system development process of mission critical systems. The product assurance process in systems of this kind requires extra attention. In this thesis, mission critical systems are space systems and the product assurance process of these systems is presented with help of space standards. The product assurance process can be supported with agile development because agile emphasizes transparency of the process and fast response to changes. Even if the development process of space systems is highly standardized and reminds waterfall model, it is still possible to adapt agile development in space systems development. This thesis aims to support the product assurance process of space systems with agile development so that the final product would be as safe and reliable as possible. The main purpose of this thesis is to examine how well product assurance is performed in Finnish space organizations and how product assurance tasks and activities can be supported with agile development. The research part of this thesis is performed in survey form.

Threat modeling a factory environment using Microsoft Security Development Lifecycle methodology

The number of security violations is increasing and a security breach could have irreversible impacts to business. There are several ways to improve organization security, but some of them may be difficult to comprehend. This thesis demystifies threat modeling as part of secure system development. Threat modeling enables developers to reveal previously undetected security issues from computer systems. It offers a structured approach for organizations to find and address threats against vulnerabilities. When implemented correctly threat modeling will reduce the amount of defects and malicious attempts against the target environment. In this thesis Microsoft Security Development Lifecycle (SDL) is introduced as an effective methodology for reducing defects in the target system. SDL is traditionally meant to be used in software development, principles can be however partially adapted to IT-infrastructure development. Microsoft threat modeling methodology is an important part of SDL and it is utilized in this thesis to find threats from the Acme Corporation’s factory environment. Acme Corporation is used as a pseudonym for a company providing high-technology consumer electronics. Target for threat modeling is the IT-infrastructure of factory’s manufacturing execution system. Microsoft threat modeling methodology utilizes STRIDE –mnemonic and data flow diagrams to find threats. Threat modeling in this thesis returned results that were important for the organization. Acme Corporation now has more comprehensive understanding concerning IT-infrastructure of the manufacturing execution system. On top of vulnerability related results threat modeling provided coherent views of the target system. Subject matter experts from different areas can now agree upon functions and dependencies of the target system. Threat modeling was recognized as a useful activity for improving security.

A software engineering approach to distributed systems for composite modeling

The goal of this thesis is to define and validate a software engineering approach for the development of a distributed system for the modeling of composite materials, based on the analysis of various existing software development methods. We reviewed the main features of: (1) software engineering methodologies; (2) distributed system characteristics and their effect on software development; (3) composite materials modeling activities and the requirements for the software development. Using the design science as a research methodology, the distributed system for creating models of composite materials is created and evaluated. Empirical experiments which we conducted showed good convergence of modeled and real processes. During the study, we paid attention to the matter of complexity and importance of distributed system and a deep understanding of modern software engineering methods and tools.

Customer Discovery and Customer Validation in Lean Software Startups

The traditional business models and the traditionally successful development methods that have been distinctive to the industrial era, do not satisfy the needs of modern IT companies. Due to the rapid nature of IT markets, the uncertainty of new innovations‟ success and the overwhelming competition with established companies, startups need to make quick decisions and eliminate wasted resources more effectively than ever before. There is a need for an empirical basis on which to build business models, as well as evaluate the presumptions regarding value and profit. Less than ten years ago, the Lean software development principles and practices became widely well-known in the academic circles. Those practices help startup entrepreneurs to validate their learning, test their assumptions and be more and more dynamical and flexible. What is special about today‟s software startups is that they are increasingly individual. There are quantitative research studies available regarding the details of Lean startups. Broad research with hundreds of companies presented in a few charts is informative, but a detailed study of fewer examples gives an insight to the way software entrepreneurs see Lean startup philosophy and how they describe it in their own words. This thesis focuses on Lean software startups‟ early phases, namely Customer Discovery (discovering a valuable solution to a real problem) and Customer Validation (being in a good market with a product which satisfies that market). The thesis first offers a sufficiently compact insight into the Lean software startup concept to a reader who is not previously familiar with the term. The Lean startup philosophy is then put into a real-life test, based on interviews with four Finnish Lean software startup entrepreneurs. The interviews reveal 1) whether the Lean startup philosophy is actually valuable for them, 2) how can the theory be practically implemented in real life and 3) does theoretical Lean startup knowledge compensate a lack of entrepreneurship experience. A reader gets familiar with the key elements and tools of Lean startups, as well as their mutual connections. The thesis explains why Lean startups waste less time and money than many other startups. The thesis, especially its research sections, aims at providing data and analysis simultaneously.

Customer Discovery and Customer Validation in Lean Software Startups

The traditional business models and the traditionally successful development methods that have been distinctive to the industrial era, do not satisfy the needs of modern IT companies. Due to the rapid nature of IT markets, the uncertainty of new innovations‟ success and the overwhelming competition with established companies, startups need to make quick decisions and eliminate wasted resources more effectively than ever before. There is a need for an empirical basis on which to build business models, as well as evaluate the presumptions regarding value and profit. Less than ten years ago, the Lean software development principles and practices became widely well-known in the academic circles. Those practices help startup entrepreneurs to validate their learning, test their assumptions and be more and more dynamical and flexible. What is special about today‟s software startups is that they are increasingly individual. There are quantitative research studies available regarding the details of Lean startups. Broad research with hundreds of companies presented in a few charts is informative, but a detailed study of fewer examples gives an insight to the way software entrepreneurs see Lean startup philosophy and how they describe it in their own words. This thesis focuses on Lean software startups‟ early phases, namely Customer Discovery (discovering a valuable solution to a real problem) and Customer Validation (being in a good market with a product which satisfies that market). The thesis first offers a sufficiently compact insight into the Lean software startup concept to a reader who is not previously familiar with the term. The Lean startup philosophy is then put into a real-life test, based on interviews with four Finnish Lean software startup entrepreneurs. The interviews reveal 1) whether the Lean startup philosophy is actually valuable for them, 2) how can the theory be practically implemented in real life and 3) does theoretical Lean startup knowledge compensate a lack of entrepreneurship experience. A reader gets familiar with the key elements and tools of Lean startups, as well as their mutual connections. The thesis explains why Lean startups waste less time and money than many other startups. The thesis, especially its research sections, aims at providing data and analysis simultaneously.

Automated UI testing. WBCT, a computer-automated user test environment tool.

Today, the user experience and usability in software application are becoming a major design issue due to the adaptation of many processes using new technologies. Therefore, the study of the user experience and usability might be included in every software development project and, thus, they should be tested to get traceable results. As a result of different testing methods to evaluate the concepts, a non-expert on the topic might have doubts on which option he/she should opt for and how to interpret the outcomes of the process. This work aims to create a process to ease the whole testing methodology based on the process created by Seffah et al. and a supporting software tool to follow the procedure of these testing methods for the user experience and usability.