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.

Intelligence in peace support operations

Finnish Defence Studies is published under the auspices of the National Defence College, and the contributions reflect the fields of research and teaching of the College. Finnish Defence Studies will occasionally feature documentation on Finnish Security Policy. Views expressed are those of the authors and do not necessarily imply endorsement by the National Defence College.

Civilian-military cooperation in crisis management operations

Finnish Defence Studies is published under the auspices of the National Defence College, and the contributions reflect the fields of research and teaching of the College. Finnish Defence Studies will occasionally feature documentation on Finnish Security Policy. Views expressed are those of the authors and do not necessarily imply endorsement by the National Defence College.

The Soviet plans for the North Western theatre of operations in 1939-1944

Finnish Defence Studies is published under the auspices of the National Defence College, and the contributions reflect the fields of research and teaching of the College. Finnish Defence Studies will occasionally feature documentation on Finnish Security Policy. Views expressed are those of the authors and do not necessarily imply endorsement by the National Defence College.

Performance improvement in mediterranean operations using risk management analysis : Case study of Containerships Group Ltd

Emerging markets of Northern Africa and Turkey provide growth opportunities for logistics service companies in the middle of low growth environment of European Union. The purpose of this research is to explore and analyze the risk factors in container shipping industry and third party logistics (3PL) services. The research empirically examined the risk factors, which are related within the interaction between these two parties in emerging markets of Mediterranean area. The previous studies have provided a valuable insight into the operational risks faced by container shipping industries. However, most of these studies have focused on one or several operational risk factors from a single point of view, and no studies have inclusively examined the possible operational risks faced in the container shipping industry from dual perspective of 3PL provider and its customers. A questionnaire has been deployed to collect related data; and the impacts of the risks were then be assessed and ranked using the method of risk mapping. Respondents were located in Turkey, Algeria, Tunisia, and Libya. Research presents the most important risk factors identified, and compares them between 3PL provider and its customers. The research also provide some risk mitigation strategies for the key risk factors, and tried to figure out a common risk picture, which guides the managers in both sides to have a better decisions and as a result, improve the performance of the container shipping operations. Challenge during project execution time was that customers identified vast amount of more risks than what was the case with logistics service operator.

Data and Inventory Management in Spare Part Business: Developing Operations in the Case Company

After sales business is an effective way to create profit and increase customer satisfaction in manufacturing companies. Despite this, some special business characteristics that are linked to these functions, make it exceptionally challenging in its own way. This Master’s Thesis examines the current situation of the data and inventory management in the case company regarding possibilities and challenges related to the consolidation of current business operations. The research examines process steps, procedures, data requirements, data mining practices and data storage management of spare part sales process, whereas the part focusing on inventory management is reviewing the current stock value and examining current practices and operational principles. There are two global after sales units which supply spare parts and issues reviewed in this study are examined from both units’ perspective. The analysis is focused on the operations of that unit where functions would be centralized by default, if change decisions are carried out. It was discovered that both data and inventory management include clear shortcomings, which result from lack of internal instructions and established processes as well as lack of cooperation with other stakeholders related to product’s lifecycle. The main product of data management was a guideline for consolidating the functions, tailored for the company’s needs. Additionally, potentially scrapped spare part were listed and a proposal of inventory management instructions was drafted. If the suggested spare part materials will be scrapped, stock value will decrease 46 percent. A guideline which was reviewed and commented in this thesis was chosen as the basis of the inventory management instructions.