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.

Information integration and its impacts on logistics performance - Using information technology and systems to facilitate information integration

Fast changing environment sets pressure on firms to share large amount of information with their customers and suppliers. The terms information integration and information sharing are essential for facilitating a smooth flow of information throughout the supply chain, and the terms are used interchangeably in research literature. By integrating and sharing information, firms want to improve their logistics performance. Firms share information with their suppliers and customers by using traditional communication methods (telephone, fax, Email, written and face-to-face contacts) and by using advanced or modern communication methods such as electronic data interchange (EDI), enterprise resource planning (ERP), web-based procurement systems, electronic trading systems and web portals. Adopting new ways of using IT is one important resource for staying competitive on the rapidly changing market (Saeed et al. 2005, 387), and an information system that provides people the information they need for performing their work, will support company performance (Boddy et al. 2005, 26). The purpose of this research has been to test and understand the relationship between information integration with key suppliers and/or customers and a firm’s logistics performance, especially when information technology (IT) and information systems (IS) are used for integrating information. Quantitative and qualitative research methods have been used to perform the research. Special attention has been paid to the scope, level and direction of information integration (Van Donk & van der Vaart 2005a). In addition, the four elements of integration (Jahre & Fabbe-Costes 2008) are closely tied to the frame of reference. The elements are integration of flows, integration of processes and activities, integration of information technologies and systems and integration of actors. The study found that information integration has a low positive relationship to operational performance and a medium positive relationship to strategic performance. The potential performance improvements found in this study vary from efficiency, delivery and quality improvements (operational) to profit, profitability or customer satisfaction improvements (strategic). The results indicate that although information integration has an impact on a firm’s logistics performance, all performance improvements have not been achieved. This study also found that the use of IT and IS have a mediocre positive relationship to information integration. Almost all case companies agreed on that the use of IT and IS could facilitate information integration and improve their logistics performance. The case companies felt that an implementation of a web portal or a data bank would benefit them - enhance their performance and increase information integration.

Formal development and quantitative verification of dependable systems

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Theorizing Formal and Informal Feedback Practices in Management Accounting Through Three Dimensions

The purpose of this doctoral thesis is to widen and develop our theoretical frameworks for discussion and analyses of feedback practices in management accounting, particularly shedding light on its formal and informal aspects. The concept of feedback in management accounting has conventionally been analyzed within cybernetic control theory, in which feedback flows as a diagnostic or comparative loop between measurable outputs and pre-set goals (see e.g. Flamholtz et al. 1985; Flamholtz 1996, 1983), i.e. as a formal feedback loop. However, the everyday feedback practices in organizations are combinations of formal and informal elements. In addition to technique-driven feedback approaches (like budgets, measurement, and reward systems) we could also categorize social feedback practices that managers see relevant and effective in the pursuit of organizational control. While cybernetics or control theories successfully capture rational and measured aspects of organizational performance and offer a broad organizational context for the analysis, many individual and informal aspects remain vague and isolated. In order to discuss and make sense of the heterogeneous field of interpretations of formal and informal feedback, both in theory and practice, dichotomous approaches seem to be insufficient. Therefore, I suggest an analytical framework of formal and informal feedback with three dimensions (3D’s): source, time, and rule. Based on an abductive analysis of the theoretical and empirical findings from an interpretive case study around a business unit called Division Steelco, the 3Dframework and formal and informal feedback practices are further elaborated vis-á-vis the four thematic layers in the organizational control model by Flamholtz et al. (1985; Flamholtz 1996, 1983): core control system, organizational structure, organizational culture, and external environment. Various personal and cultural meanings given to the formal and informal feedback practices (“feedback as something”) create multidimensional interpretative contexts. Multidimensional frameworks aim to capture and better understand both the variety of interpretations and their implications to the functionality of feedback practices, important in interpretive research.

Preparing for CRIS: Challenges and Opportunities for Systems Integration at Finnish Universities

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

Decision making and decision support in service systems

This thesis is a literature study that develops a conceptual model of decision making and decision support in service systems. The study is related to the Ä-Logi, Intelligent Service Logic for Welfare Sector Services research project, and the objective of the study is to develop the necessary theoretical framework to enable further research based on the research project results and material. The study first examines the concepts of service and service systems, focusing on understanding the characteristics of service systems and their implications for decision making and decision support to provide the basis for the development of the conceptual model. Based on the identified service system characteristics, an integrated model of service systems is proposed that views service systems through a number of interrelated perspectives that each offer different, but complementary, implications on the nature of decision making and the requirements for decision support in service systems. Based on the model, it is proposed that different types of decision making contexts can be identified in service systems that may be dominated by different types of decision making processes and where different types of decision support may be required, depending on the characteristics of the decision making context and its decision making processes. The proposed conceptual model of decision making and decision support in service systems examines the characteristics of decision making contexts and processes in service systems, and their typical requirements for decision support. First, a characterization of different types of decision making contexts in service systems is proposed based on the Cynefin framework and the identified service system characteristics. Second, the nature of decision making processes in service systems is proposed to be dual, with both rational and naturalistic decision making processes existing in service systems, and having an important and complementary role in decision making in service systems. Finally, a characterization of typical requirements for decision support in service systems is proposed that examines the decision support requirements associated with different types of decision making processes in characteristically different types of decision making contexts. It is proposed that decision support for the decision making processes that are based on rational decision making can be based on organizational decision support models, while decision support for the decision making processes that are based on naturalistic decision making should be based on supporting the decision makers’ situation awareness and facilitating the development of their tacit knowledge of the system and its tasks. Based on the proposed conceptual model a further research process is proposed. The study additionally provides a number of new perspectives on the characteristics of service systems, and the nature of decision making and requirements for decision support in service systems that can potentially provide a basis for further discussion and research, and support the practice alike.