Methods for construction and analysis of computational models in systems biology : applications to the modelling of the heat shock response and the self-assembly of intermediate filaments

Systems biology is a new, emerging and rapidly developing, multidisciplinary research field that aims to study biochemical and biological systems from a holistic perspective, with the goal of providing a comprehensive, system- level understanding of cellular behaviour. In this way, it addresses one of the greatest challenges faced by contemporary biology, which is to compre- hend the function of complex biological systems. Systems biology combines various methods that originate from scientific disciplines such as molecu- lar biology, chemistry, engineering sciences, mathematics, computer science and systems theory. Systems biology, unlike “traditional” biology, focuses on high-level concepts such as: network, component, robustness, efficiency, control, regulation, hierarchical design, synchronization, concurrency, and many others. The very terminology of systems biology is “foreign” to “tra- ditional” biology, marks its drastic shift in the research paradigm and it indicates close linkage of systems biology to computer science. One of the basic tools utilized in systems biology is the mathematical modelling of life processes tightly linked to experimental practice. The stud- ies contained in this thesis revolve around a number of challenges commonly encountered in the computational modelling in systems biology. The re- search comprises of the development and application of a broad range of methods originating in the fields of computer science and mathematics for construction and analysis of computational models in systems biology. In particular, the performed research is setup in the context of two biolog- ical phenomena chosen as modelling case studies: 1) the eukaryotic heat shock response and 2) the in vitro self-assembly of intermediate filaments, one of the main constituents of the cytoskeleton. The range of presented approaches spans from heuristic, through numerical and statistical to ana- lytical methods applied in the effort to formally describe and analyse the two biological processes. We notice however, that although applied to cer- tain case studies, the presented methods are not limited to them and can be utilized in the analysis of other biological mechanisms as well as com- plex systems in general. The full range of developed and applied modelling techniques as well as model analysis methodologies constitutes a rich mod- elling framework. Moreover, the presentation of the developed methods, their application to the two case studies and the discussions concerning their potentials and limitations point to the difficulties and challenges one encounters in computational modelling of biological systems. The problems of model identifiability, model comparison, model refinement, model inte- gration and extension, choice of the proper modelling framework and level of abstraction, or the choice of the proper scope of the model run through this thesis.

Construction Plan Image Service for Mobile Devices

The forthcoming media revolution of exchanging paper documents to digital media in construction engineering requires new tools to be developed. The basis of this bachelor’s thesis was to explore the preliminary possibilities of exporting imagery from a Building Information Modelling –software to a mobile phone on a construction yard. This was done by producing a Web Service which uses the design software’s Application Programming Interface to interact with a structures model in order to produce the requested imagery. While mobile phones were found lacking as client devices, because of limited processing power and small displays, the implementation showed that the Tekla Structures API can be used to automatically produce various types of imagery. Web Services can be used to transfer this data to the client. Before further development the needs of the contractor, benefits for the building master and inspector and the full potential of the BIM-software need to be mapped out with surveys.

Animal Lovers, Bridge-Builders, and Supervising Watchdogs: Framing and Civil Society Construction by Japanese Pro-Animal Organizations in the Kansai and Tokyo Areas

Unlike their counterparts in Europe and America, the citizen organizations acting for the well-being of animals in Japan have not received scholarly attention. In this research, I explore the activities of twelve Japanese pro-animal organizations in Tokyo and Kansai area from the perspective of social movement and civil society studies. The concept of a ‘pro-animal organization’ is used to refer generally to the collectives promoting animal well-being. By using the collective action frame analysis and the three core framing tasks – diagnostic, prognostic, and motivational – as the primarily analytical tools, I explore the grievances, tactics, motivational means, constructions of agency and identity as well as framing of civil society articulated in the newsletters and the interviews of the twelve organizations I interviewed in Japan in 2010. As the frame construction is always done in relation to the social and political context, I study how the organizations construct their roles as civil society actors in relation to other actors, such as the state, and the idea of citizen activism. The deficiencies in the animal welfare law and lack of knowledge among the public are identified as the main grievances. The primary tactic to overcome these problems was to educate and inform the citizens and authorities, because most organizations lack the channels to influence politically. The audiences were mostly portrayed as either ignorant bystanders or potential adherents. In order to motivate people to join their cause and to enforce the motivation within the organization, the organizations emphasized their uniqueness, proved their efficiency, claimed credit and celebrated even small improvements. The organizations tended to create three different roles for citizen pro-organizations in civil society: reactive, apolitical and emphatic animal lovers concentrating on saving individual animals, proactive, educative bridge-builders seeking to establish equal collaborative relations with authorities, and corrective, supervising watchdogs demanding change in delinquencies offending animal rights. Based on the results of this research, I suggest that by studying how and why the different relations between civil society and the governing actors of the state are constructed, a more versatile approach to citizens’ activism in its context can be achieved.

Segregation of powder mixtures in silos with particular reference to dry mineral-based construction materials

Segregering eller segregation är ett fenomen som kan förekomma inom olika områden av samhället. Inom samhällsvetenskaperna kan segregering definieras som det rumsliga åtskiljandet av befolkningsgrupper på urval av ras eller etniskt ursprung, kön, social härkomst, religion, ålder, yrke, osv. Segregering av befolkningsgrupper sker ofta mer eller mindre frivilligt och är motsatsen till integration. Inom partikelteknologi definieras segregering oftast som det rumsliga åtskiljandet av beståndsdelarna i en blandning av olika partiklar. Segregering sker då på urval av bl.a. partiklarnas storlek, densitet, form, elektrostatiska eller mekaniska egenskaper, och kan beskrivas som motsatsen till blandning. Segregeringsmekanismer används för att förklara hur och varför en partikelblandning segregerar samt vad slutresultatet i form av den rumsliga fördelningen av partiklarna blir till följd av att blandningen utsetts för en viss behandling. I denna avhandling har segregering av partikelblandningar och speciellt torra mineralbaserade byggmaterial (t.ex. murbruk) till följd av lagring i siloer studerats. Vid industriell produktion av mineralbaserade byggmaterial används siloer för korttidslagring av slutprodukterna precis innan förpackning. Segregering leder till kraftiga variationer i sammansättningen för partikelströmmen ut ur silon, vilket gör att slutprodukterna inte uppfyller kvalitetskraven och kan därmed inte säljas till kunder. Detta leder till arbetsam och dyr bearbetning (återcirkulation) av produkterna med påföljder för produktionsekonomin samt hållbara utvecklingen. I avhandlingen identifierades de väsentligaste segregeringsmekanismerna för torra mineralbaserade byggmaterial i siloer. Dessutom klargjordes effekterna av materialegenskaper, processbetingelser och siloparametrar. Slutligen behandlas möjliga åtgärder för minskning av partikelsegregering i siloer samt tillämpning av matematiska metoder för simulering av partikelflöden med hjälp av datorer.

The Dark Side of International Business? Stakeholder Approach to Human Trafficking in Finnish Construction and Service Sectors

Human trafficking is not a new phenomenon. It has existed in various forms for ages around the world. Some researchers have even compared it to slavery, calling it the modern form of slavery in the 21st century. This study is particularly interested in the role of work-related human trafficking in Finnish business. In order for something to be called work-related human trafficking, the concepts of forced labour and human trafficking have to overlap. From the economic point of view, human trafficking is governed by the laws of supply and demand. In many countries the global pressure on cutting costs has created two trends: the increased supply of migrant workers and the deregulation of labour markets. These competitive pressures can have an adverse impact on the conditions of employment and, in the worst cases, can lead to forced labour and trafficking. In fact, trafficking has become one of the most profitable illicit industries worldwide, generating tremendous profits due to its low costs and huge profits. Therefore, it is important to investigate the phenomenon from the business point of view. This study is a qualitative research conducted by using theme interviews as a research approach. Altogether 13 interviews have been conducted and some secondary data has been used in order to find out what the role of human trafficking is in Finnish business. The special sectors investigated are the Finnish construction and service sectors. The theory framework used in this study follows the stakeholder approach. The relevant stakeholder groups for this study are: ‘institutions and authorities’, ‘law enforcement’, ‘management’ and ‘employees – potential victims’ of trafficking. With the help of these stakeholder groups, a holistic picture of the phenomenon is formed. It can be concluded that the role of human trafficking is complicated but it does exist in Finnish business. It appears in low-cost business sectors where the demand for cheap labour is high. Thus, often the victims are foreigners who do not know the culture or the Finnish conditions of employment. Especially smaller Finnish companies are at risk of getting involved in human trafficking or related exploitation cases since monitoring is much more scarce in these firms than in larger companies. The risk of human trafficking and exploitation is also higher at the bottom of the complicated subcontracting chains or when using foreign recruitment agencies. Thus, the study believes that active and intensive collaboration between the company’s different stakeholder groups is needed in order to prevent work-related human trafficking from flourishing in Finland.

Future trends of Finnish cement based construction

The construction material sector, as a capital intensive industry, is highly vulnerable to rapid fluctuations in the economic cycles. In Finland this was witnessed especially during the late 2000s, as in 2007 and 2008 the demand for several construction materials exceeded their supply and right after this, in 2009 the demand collapsed fast as a result of an international recession. These factors brought about the need to study the future trends of the market place of the commissioning company, Finnsementti Oy. As reliable short term market forecasts for the sector are difficult to compose, the study concentrates primarily in examining and identifying the trends that are likely to affect the Finnish cement industry, and as an extension, the concrete industry in a frame of 10 to 15 years. The study’s scope comprehends also the examination of the domestic construction sector, as it represents the end user industry of both cement and concrete. These motives for the study produce the research problem, which is to conduct a trend analysis for cement based building in the Finnish market area in the 2020s. The theoretical frame for composing a trend analysis in the case of this study is twofold. This is due to the fact that both, the macro and micro environments of the examined industries are studied. The main methods used are the PESTE-model (macro) and Porter’s five forces model (micro). The study applies a qualitative approach and the data is gathered by interviewing a group of experts from the cement, concrete and construction industries. The result of the paper is an overall trend analysis for the Finnish cement based building sector, which is based on ‘sub trend analyses’ concerning four identified sub-sectors of the Finnish construction industry. The results are a combination of findings from these sub-sectors and the analyzed data that deals with the studied sector’s macro and micro environment. The conclusions provide an overall picture of the examined sectors’ potential future as a whole and by defined sub-sectors of the construction industry. The recognition of future trends in different areas of the construction industry can be applied as a means for an industry actor’s decision making and in estimating the types of construction that are likely to grow or decline. Finally, based on the analyzed data and conclusions, the commissioning company is provided with a brief SWOT analysis, that provides additional tools for decision making and planning processes regarding the future.

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.

Integration of learning supportive applications into the development of the e-portfolio construction process

The portfolio as a means of demonstrating personal skills has lately been gaining prominence among technology students. This is partially due to the introduction of electronic portfolios, or e-portfolios. As platforms for e-portfolio management with different approaches have been introduced, the learning cycle, traditional portfolio pedagogy, and learner centricity have sometimes been forgotten, and as a result, the tools have been used for the most part as data depositories. The purpose of this thesis is to show how the construction of e-portfolios of IT students can be supported by institutions through the usage of different tools that relate to study advising, teaching, and learning. The construction process is presented as a cycle based on learning theories. Actions related to the various phases of the e-portfolio construction process are supported by the implementation of software applications. To maximize learner-centricity and minimize the intervention of the institution, the evaluated and controlled actions for these practices can be separated from the e-portfolios, leaving the construction of the e-portfolio to students. The main contributions of this thesis are the implemented applications, which can be considered to support the e-portfolio construction by assisting in planning, organizing, and reflecting activities. Eventually, this supports the students in their construction of better and more extensive e-portfolios. The implemented tools include 1) JobSkillSearcher to help students’ recognition of the demands of the ICT industry regarding skills, 2) WebTUTOR to support students’ personal study planning, 3) Learning Styles to determine students' learning styles, and 4) MyPeerReview to provide a platform on which to carry out anonymous peer review processes in courses. The most visible outcome concerning the e-portfolio is its representation, meaning that one can use it to demonstrate personal achievements at the time of seeking a job and gaining employment. Testing the tools and the selected open-source e-portfolio application indicates that the degree of richness of e-portfolio content can be increased by using the implemented applications.

Creating risk measurement model to project portfolio management in construction company

This thesis was carried out as a case study of a company YIT in order to clarify the sev-erest risks for the company and to build a method for project portfolio evaluation. The target organization creates new living environment by constructing residential buildings, business premises, infrastructure and entire areas worth for EUR 1.9 billion in the year 2013. Company has noted project portfolio management needs more information about the structure of project portfolio and possible influences of market shock situation. With interviews have been evaluated risks with biggest influence and most appropriate metrics to examine. The major risks for the company were evaluated by interviewing the executive staff. At the same time, the most appropriate risk metrics were considered. At the moment sales risk was estimated to have biggest impact on company‟s business. Therefore project port-folio evaluation model was created and three different scenarios for company‟s future were created in order to identify the scale of possible market shock situation. The created model is tested with public and descriptive figures of YIT in a one-year-long market shock and the impact on different metrics was evaluated. Study was conducted using con-structive research methodology. Results indicate that company has notable sales risk in certain sections of business portfolio.