Computational models for and from biology : simple gene assembly and reaction systems

The advancement of science and technology makes it clear that no single perspective is any longer sufficient to describe the true nature of any phenomenon. That is why the interdisciplinary research is gaining more attention overtime. An excellent example of this type of research is natural computing which stands on the borderline between biology and computer science. The contribution of research done in natural computing is twofold: on one hand, it sheds light into how nature works and how it processes information and, on the other hand, it provides some guidelines on how to design bio-inspired technologies. The first direction in this thesis focuses on a nature-inspired process called gene assembly in ciliates. The second one studies reaction systems, as a modeling framework with its rationale built upon the biochemical interactions happening within a cell. The process of gene assembly in ciliates has attracted a lot of attention as a research topic in the past 15 years. Two main modelling frameworks have been initially proposed in the end of 1990s to capture ciliates’ gene assembly process, namely the intermolecular model and the intramolecular model. They were followed by other model proposals such as templatebased assembly and DNA rearrangement pathways recombination models. In this thesis we are interested in a variation of the intramolecular model called simple gene assembly model, which focuses on the simplest possible folds in the assembly process. We propose a new framework called directed overlap-inclusion (DOI) graphs to overcome the limitations that previously introduced models faced in capturing all the combinatorial details of the simple gene assembly process. We investigate a number of combinatorial properties of these graphs, including a necessary property in terms of forbidden induced subgraphs. We also introduce DOI graph-based rewriting rules that capture all the operations of the simple gene assembly model and prove that they are equivalent to the string-based formalization of the model. Reaction systems (RS) is another nature-inspired modeling framework that is studied in this thesis. Reaction systems’ rationale is based upon two main regulation mechanisms, facilitation and inhibition, which control the interactions between biochemical reactions. Reaction systems is a complementary modeling framework to traditional quantitative frameworks, focusing on explicit cause-effect relationships between reactions. The explicit formulation of facilitation and inhibition mechanisms behind reactions, as well as the focus on interactions between reactions (rather than dynamics of concentrations) makes their applicability potentially wide and useful beyond biological case studies. In this thesis, we construct a reaction system model corresponding to the heat shock response mechanism based on a novel concept of dominance graph that captures the competition on resources in the ODE model. We also introduce for RS various concepts inspired by biology, e.g., mass conservation, steady state, periodicity, etc., to do model checking of the reaction systems based models. We prove that the complexity of the decision problems related to these properties varies from P to NP- and coNP-complete to PSPACE-complete. We further focus on the mass conservation relation in an RS and introduce the conservation dependency graph to capture the relation between the species and also propose an algorithm to list the conserved sets of a given reaction system.

Improving productivity by developing knowledge management practices for a consulting company

The objective of the research was to identify knowledge conversion states in consultancy sales and delivery processes for the company’s one business unit, to know where to store certain types of information and knowledge, and to create best practices for the company’s knowledge management activities in the selected business processes. The used research methodology was action research. The current business processes were analyzed by interviewing people involved in them. The results were documented and catego- rized, and based on them the target states of the processes were developed. Knowledge man- agement activities were integrated to the business processes. The main findings of the research were that roles and responsibilities in the processes were not clear to people, information systems did not fully support individuals and time was wasted searching for information and knowledge. There were also many variations of how the processes actually realized, which affected the overall quality of the process. The conclusions of the research were that knowledge management activities should be high- lighted in businesses where knowledge workers are the main assets of the company. Knowledge management practices can be supported by company culture, leadership and in- formation systems. However, one main factor is each individual’s willingness to share knowledge. By integrating knowledge management activities to business processes and hav- ing information systems supporting knowledge management, individual productivity can be improved.

Nettikoulussa – Opettajien käsityksiä nettikasvatuksesta ja nuorten nettikulttuurista

Tutkimuksessa kuvataan opettajien käsityksiä nettikasvatuksesta ja nuorten nettikulttuurista. Tehtävänä on kuvata kuuden opettajan näkemyksiä nuorten nettimaailmasta sekä oppilaan, että kasvattajan näkökulmasta. Tutkimus on lähtökohdiltaan kvalitatiivinen. Tutkimuksen metodologisena viitekehyksenä käytetään fenomenografista lähestymistapaa. Tutkimuksen tulosten mukaan opettajien käsitykset nuorten nettikulttuurista olivat hyvin moninaiset. Opettajien käsityksiä nuorten nettikulttuurista kuvasti vahva huoli nuorten arvoista ja suhteestaan mediakriittisyyteen. Nettikulttuuriin liittyen huolenaiheena olivat myös nuorten nettiriippuvuus, sekä huoli liikunnan vähentymisestä. Nämä aiheet heijastuivat vahvasti opettajien omiin nuoruudenajan kokemuksiin nuorisokulttuurista. Toisaalta internet ja sosiaalinen media nähtiin mahdollistavana, yhdistävänä tekijänä, joka heijastui koulun arkeen nuorten avoimuutena ja kokemusten jakamisena. Opettajien käsityksissä heijastui myös kulttuurin kokonaisvaltaisuus; miten Internet ja sosiaalinen media syö kulttuurin itseensä, kun kaikki toiminta siirtyy verkkoon. Nettikasvatuksen opettajat kokivat olevan hyvin harkinnanvaraista ja riippuvan omasta kiinnostuksesta aihetta kohtaan. Nettikasvattajina opettajat kokivat tärkeäksi mediakasvatuksen ja kriittisen tiedon etsinnän taidot. Vastuu ja sen jakaminen olivat merkittävä tekijä opettajien puhuessa nettikasvatuksestaan ja roolistaan siinä. Opettajat eivät halunneet mennä kodin tehtävien edelle, mutta rajan määrittäminen oli haasteellista. Vastavuoroisuus nettikasvatuksessa ja teknologisessa koulumaail-massa nähtiin hyvin merkittävä.

Palkitsemisen rooli varainhoitoyrityksessä

Tässä tutkielmassa keskityttiin varainhoitoyrityksen aineellisiin ja aineettomiin palkitsemistapoihin ja arvioitiin niiden vaikutusta tarkasteltavan liiketoimintayksikön tavoitteiden täyttymiseen. Tutkimuksessa tutkittiin myös työmotivaatioon vaikuttavia tekijöitä sekä mahdollisia parannuksia toteutettavaan palkitsemiseen. Tutkimus toteutettiin tapaustutkimuksena laadullisen tutkimuksen keinoin.

The Impact of Event Marketing on Brand Awareness in eSport Industry

The purpose of this qualitative research is to study what is the impact of event marketing on brand awareness in the context of electronic sport industry. Based on the research questions, the theoretical framework will be developed. This research will analyze earlier theories, and also searching more fresh literature to explain the current phenomenon in the eSport industry. In the empirical part, there were total of five case companies interviewed. The context of this research is eSport, which has its own chapter. The theoretical part of the thesis focuses on event marketing and brand awareness. In this research, event marketing is analyzed from the event organizers perspective. In some occasions, event exhibitors’ perspective is also analyzed. In brand awareness, the focus is how to create a brand recognizable, recalled and from there top of mind in consumers’ minds. The results of this research revealed that many companies’ struggles on getting their brand recognizable. Some of the case companies lacks a strategy and don’t exactly know the core values of their customers. However some of the case companies were opposite. One reason behind this is that some of them has experience on the field and the companies have resources that covers them. Also the current strong brand has clearly a positive affect on their business.

Valukappaleiden valmistusprosessin kapeikot teräsvalimossa

Teräsvalimon toimitusprosessissa toimitusvarmuus on tärkeä tuotannon tunnusluku. Valimotuotannossa olevien lukuisten muuttujien vuoksi tuotannonsuunnittelu ja läpivirtauksen hallinta on haasteellista. Tuotteiden, valumateriaalien ja näiden yhdistelmien suuri yhtäaikainen määrä tuotannossa vaikeuttaa tuotannon ennustettavuutta sekä vaikuttaa läpivirtaukseen ja toimitusvarmuuteen. Lisäksi tuotannon eri työvaiheissa ilmenevät kapeikot rajoittavat läpivirtausta ja kasvattavat läpimenoaikoja. Kapeikkoja voidaan hyödyntää tuotannonohjauksessa jos kapeikot ovat selkeästi havaittavissa. Kapasiteetin siirtäminen ei-kapeikosta kapeikkoon lisää tuotannon läpivirtausta. Pelkkä kapeikkojen hallinta ei paranna toimitusvarmuutta jos keskeneräisen tuotannon määrä on suuri ja järjestys väärä. Tuotannon työkuormien visuaalisuuden parantaminen kaikilla työvaiheilla antaa mahdollisuuksia ohjata tuotantoa tehokkaammin. Kandidaatintyössä on tarkasteltu teräsvalimon valmistusprosessia ja selvitetty tuotannon eri vaiheissa ilmeneviä kapeikkoja. Selvitystyössä hyödynnettiin TOC-analyysiä. Keskeneräisen tuotannon määrää mitattiin useilla otannoilla eri työvaiheiden kohdalla. Tuloksia analysoimalla löydettiin tuotannon ongelmakohdat ja niihin tarvittavat kehitystoimenpiteet.

Convenience of scallops in plate structures

In this thesis was performed comprehensive study about the convenience of scallops in plate structures. A literature review was performed and lack of knowledge was fulfilled with fatigue tests performed in the laboratory of Steel Structures at the Lappeenranta University of Technology and with finite element method. The aim of this thesis was to produce design guidance for the use of scallops for different structural details and different loading conditions. An additional aim was to include more precise instructions for scallop design to produce good fatigue resistance and appropriate manufacturing quality. The literature review was performed searching bridge engineering and maritime standards and design guides and studies from scientific databases and reference lists from the literature of this field. Fatigue tests were used to research the effect of using scallops or not using scallops to fatigue strength of bracket specimen. Tests were performed on three specimens with different scallop radii and to five specimens without scallops with different weld penetration depths. Finite element method using solid elements, symmetry and submodels was used to determine stress concentration factors for I-beams with scallops. Stresses were defined with hot spot stress method. Choosing to use a scallop or not in the structure is affected by many factors, such as structural and loading conditions and manufacturability. As a rule of thumb, scallops should be avoided because those cause stress concentration points to the structure and take a lot of time to manufacture. When scallops are not used, good quality welding should be provided and full weld penetration is recommended to be used in load carrying corner weld areas. In some cases, it is advisable to use scallops. In that case, circular scallops are recommended to be used and radius should be chosen from fatigue strength or manufacturing point of view.

GIS-based approach for optimization of onshore wind park infrastructure alignment in Finland

Wind power is a rapidly developing, low-emission form of energy production. In Fin-land, the official objective is to increase wind power capacity from the current 1 005 MW up to 3 500–4 000 MW by 2025. By the end of April 2015, the total capacity of all wind power project being planned in Finland had surpassed 11 000 MW. As the amount of projects in Finland is record high, an increasing amount of infrastructure is also being planned and constructed. Traditionally, these planning operations are conducted using manual and labor-intensive work methods that are prone to subjectivity. This study introduces a GIS-based methodology for determining optimal paths to sup-port the planning of onshore wind park infrastructure alignment in Nordanå-Lövböle wind park located on the island of Kemiönsaari in Southwest Finland. The presented methodology utilizes a least-cost path (LCP) algorithm for searching of optimal paths within a high resolution real-world terrain dataset derived from airborne lidar scannings. In addition, planning data is used to provide a realistic planning framework for the anal-ysis. In order to produce realistic results, the physiographic and planning datasets are standardized and weighted according to qualitative suitability assessments by utilizing methods and practices offered by multi-criteria evaluation (MCE). The results are pre-sented as scenarios to correspond various different planning objectives. Finally, the methodology is documented by using tools of Business Process Management (BPM). The results show that the presented methodology can be effectively used to search and identify extensive, 20 to 35 kilometers long networks of paths that correspond to certain optimization objectives in the study area. The utilization of high-resolution terrain data produces a more objective and more detailed path alignment plan. This study demon-strates that the presented methodology can be practically applied to support a wind power infrastructure alignment planning process. The six-phase structure of the method-ology allows straightforward incorporation of different optimization objectives. The methodology responds well to combining quantitative and qualitative data. Additional-ly, the careful documentation presents an example of how the methodology can be eval-uated and developed as a business process. This thesis also shows that more emphasis on the research of algorithm-based, more objective methods for the planning of infrastruc-ture alignment is desirable, as technological development has only recently started to realize the potential of these computational methods.

Viability of part cargoes in tramp shipping company’s routing and scheduling decisions

Operational excellence of individual tramp shipping companies is important in today’s market, where competition is intense, freight revenues are modest and capital costs high due to global financial crisis, and tighter regulatory framework is generating additional costs and challenges to the industry. This thesis concentrates on tramp shipping, where a tramp operator in a form of an individual case company, specialized in short-sea shipping activities in the Baltic Sea region, is searching ways to map their current fleet operations and better understand potential ways to improve the overall routing and scheduling decisions. The research problem is related to tramp fleet planning where several cargoes are carried on board at the same time, which are here systematically referred to as part cargoes. The purpose is to determine the pivotal dimensions and characteristics of these part cargo operations in tramp shipping, and offer both the individual case company and wider research community better understanding of potential risks and benefits related to utilization of part cargo operations. A mixed method research approach is utilized in this research, as the objectives are related to complex, real-life business practices in the field of supply chain management and more specifically, maritime logistics. A quantitative analysis of different voyage scenarios is executed, including alternative voyage legs with varying cost structure and customer involvement. An on-line-based questionnaire designed and prepared by case company’s decision group again provides desired data of predominant attitudes and views of most important industrial customers regarding the part cargo-related operations and potential future utilization of this business model. The results gained from these quantitative methods are complied with qualitative data collection tools, along with suitable secondary data sources. Based on results and logical analysis of different data sources, a framework for characterizing the different aspects of part cargo operations is developed, utilizing both existing research and empirical investigation of the phenomenon. As conclusions, part cargoes have the ability to be part of viable fleet operations, and even increase flexibility among the fleet to a certain extent. Naturally, several hinderers for this development is recognized as well, such as potential issues with information gathering and sharing, inefficient port activities, and increased transit times.