Instant Storyboarding

This thesis aims at empowering software customers with a tool to build software tests them selves, based on a gradual refinement of natural language scenarios into executable visual test models. The process is divided in five steps: 1. First, a natural language parser is used to extract a graph of grammatical relations from the textual scenario descriptions. 2. The resulting graph is transformed into an informal story pattern by interpreting structurization rules based on Fujaba Story Diagrams. 3. While the informal story pattern can already be used by humans the diagram still lacks technical details, especially type information. To add them, a recommender based framework uses web sites and other resources to generate formalization rules. 4. As a preparation for the code generation the classes derived for formal story patterns are aligned across all story steps, substituting a class diagram. 5. Finally, a headless version of Fujaba is used to generate an executable JUnit test. The graph transformations used in the browser application are specified in a textual domain specific language and visualized as story pattern. Last but not least, only the heavyweight parsing (step 1) and code generation (step 5) are executed on the server side. All graph transformation steps (2, 3 and 4) are executed in the browser by an interpreter written in JavaScript/GWT. This result paves the way for online collaboration between global teams of software customers, IT business analysts and software developers.

Modellbasiertes Service Level Management verteilter Anwendungssysteme

Zur Senkung von Kosten werden in vielen Unternehmen Dienstleistungen, die nicht zur Kernkompetenz gehören, an externe Dienstleister ausgelagert. Dieser Prozess wird auch als Outsourcing bezeichnet. Die dadurch entstehenden Abhängigkeiten zu den externen Dienstleistern werden mit Hilfe von Service Level Agreements (SLAs) vertraglich geregelt. Die Aufgabe des Service Level Managements (SLM) ist es, die Einhaltung der vertraglich fixierten Dienstgüteparameter zu überwachen bzw. sicherzustellen. Für eine automatische Bearbeitung ist daher eine formale Spezifikation von SLAs notwendig. Da der Markt eine Vielzahl von unterschiedlichen SLM-Werkzeugen hervorgebracht hat, entstehen in der Praxis Probleme durch proprietäre SLA-Formate und fehlende Spezifikationsmethoden. Daraus resultiert eine Werkzeugabhängigkeit und eine limitierte Wiederverwendbarkeit bereits spezifizierter SLAs. In der vorliegenden Arbeit wird ein Ansatz für ein plattformunabhängiges Service Level Management entwickelt. Ziel ist eine Vereinheitlichung der Modellierung, so dass unterschiedliche Managementansätze integriert und eine Trennung zwischen Problem- und Technologiedomäne erreicht wird. Zudem wird durch die Plattformunabhängigkeit eine hohe zeitliche Stabilität erstellter Modelle erreicht. Weiteres Ziel der Arbeit ist, die Wiederverwendbarkeit modellierter SLAs zu gewährleisten und eine prozessorientierte Modellierungsmethodik bereitzustellen. Eine automatisierte Etablierung modellierter SLAs ist für eine praktische Nutzung von entscheidender Relevanz. Zur Erreichung dieser Ziele werden die Prinzipien der Model Driven Architecture (MDA) auf die Problemdomäne des Service Level Managements angewandt. Zentrale Idee der Arbeit ist die Definition von SLA-Mustern, die konfigurationsunabhängige Abstraktionen von Service Level Agreements darstellen. Diese SLA-Muster entsprechen dem Plattformunabhängigen Modell (PIM) der MDA. Durch eine geeignete Modelltransformation wird aus einem SLA-Muster eine SLA-Instanz generiert, die alle notwendigen Konfigurationsinformationen beinhaltet und bereits im Format der Zielplattform vorliegt. Eine SLA-Instanz entspricht damit dem Plattformspezifischen Modell (PSM) der MDA. Die Etablierung der SLA-Instanzen und die daraus resultierende Konfiguration des Managementsystems entspricht dem Plattformspezifischen Code (PSC) der MDA. Nach diesem Schritt ist das Managementsystem in der Lage, die im SLA vereinbarten Dienstgüteparameter eigenständig zu überwachen. Im Rahmen der Arbeit wurde eine UML-Erweiterung definiert, die eine Modellierung von SLA-Mustern mit Hilfe eines UML-Werkzeugs ermöglicht. Hierbei kann die Modellierung rein graphisch als auch unter Einbeziehung der Object Constraint Language (OCL) erfolgen. Für die praktische Realisierung des Ansatzes wurde eine Managementarchitektur entwickelt, die im Rahmen eines Prototypen realisiert wurde. Der Gesamtansatz wurde anhand einer Fallstudie evaluiert.

Design, implementation and application of a generic framework for integrated regional land-use modeling

Land use is a crucial link between human activities and the natural environment and one of the main driving forces of global environmental change. Large parts of the terrestrial land surface are used for agriculture, forestry, settlements and infrastructure. Given the importance of land use, it is essential to understand the multitude of influential factors and resulting land use patterns. An essential methodology to study and quantify such interactions is provided by the adoption of land-use models. By the application of land-use models, it is possible to analyze the complex structure of linkages and feedbacks and to also determine the relevance of driving forces. Modeling land use and land use changes has a long-term tradition. In particular on the regional scale, a variety of models for different regions and research questions has been created. Modeling capabilities grow with steady advances in computer technology, which on the one hand are driven by increasing computing power on the other hand by new methods in software development, e.g. object- and component-oriented architectures. In this thesis, SITE (Simulation of Terrestrial Environments), a novel framework for integrated regional sland-use modeling, will be introduced and discussed. Particular features of SITE are the notably extended capability to integrate models and the strict separation of application and implementation. These features enable efficient development, test and usage of integrated land-use models. On its system side, SITE provides generic data structures (grid, grid cells, attributes etc.) and takes over the responsibility for their administration. By means of a scripting language (Python) that has been extended by language features specific for land-use modeling, these data structures can be utilized and manipulated by modeling applications. The scripting language interpreter is embedded in SITE. The integration of sub models can be achieved via the scripting language or by usage of a generic interface provided by SITE. Furthermore, functionalities important for land-use modeling like model calibration, model tests and analysis support of simulation results have been integrated into the generic framework. During the implementation of SITE, specific emphasis was laid on expandability, maintainability and usability. Along with the modeling framework a land use model for the analysis of the stability of tropical rainforest margins was developed in the context of the collaborative research project STORMA (SFB 552). In a research area in Central Sulawesi, Indonesia, socio-environmental impacts of land-use changes were examined. SITE was used to simulate land-use dynamics in the historical period of 1981 to 2002. Analogous to that, a scenario that did not consider migration in the population dynamics, was analyzed. For the calculation of crop yields and trace gas emissions, the DAYCENT agro-ecosystem model was integrated. In this case study, it could be shown that land-use changes in the Indonesian research area could mainly be characterized by the expansion of agricultural areas at the expense of natural forest. For this reason, the situation had to be interpreted as unsustainable even though increased agricultural use implied economic improvements and higher farmers' incomes. Due to the importance of model calibration, it was explicitly addressed in the SITE architecture through the introduction of a specific component. The calibration functionality can be used by all SITE applications and enables largely automated model calibration. Calibration in SITE is understood as a process that finds an optimal or at least adequate solution for a set of arbitrarily selectable model parameters with respect to an objective function. In SITE, an objective function typically is a map comparison algorithm capable of comparing a simulation result to a reference map. Several map optimization and map comparison methodologies are available and can be combined. The STORMA land-use model was calibrated using a genetic algorithm for optimization and the figure of merit map comparison measure as objective function. The time period for the calibration ranged from 1981 to 2002. For this period, respective reference land-use maps were compiled. It could be shown, that an efficient automated model calibration with SITE is possible. Nevertheless, the selection of the calibration parameters required detailed knowledge about the underlying land-use model and cannot be automated. In another case study decreases in crop yields and resulting losses in income from coffee cultivation were analyzed and quantified under the assumption of four different deforestation scenarios. For this task, an empirical model, describing the dependence of bee pollination and resulting coffee fruit set from the distance to the closest natural forest, was integrated. Land-use simulations showed, that depending on the magnitude and location of ongoing forest conversion, pollination services are expected to decline continuously. This results in a reduction of coffee yields of up to 18% and a loss of net revenues per hectare of up to 14%. However, the study also showed that ecological and economic values can be preserved if patches of natural vegetation are conservated in the agricultural landscape. -----------------------------------------------------------------------

Dual retrieval in conceptual information systems

Conceptual Information Systems provide a multi-dimensional conceptually structured view on data stored in relational databases. On restricting the expressiveness of the retrieval language, they allow the visualization of sets of realted queries in conceptual hierarchies, hence supporting the search of something one does not have a precise description, but only a vague idea of. Information Retrieval is considered as the process of finding specific objects (documents etc.) out of a large set of objects which fit to some description. In some data analysis and knowledge discovery applications, the dual task is of interest: The analyst needs to determine, for a subset of objects, a description for this subset. In this paper we discuss how Conceptual Information Systems can be extended to support also the second task.

Conceptual structures represented by conceptual graphs and formal concept analysis

Conceptual Graphs and Formal Concept Analysis have in common basic concerns: the focus on conceptual structures, the use of diagrams for supporting communication, the orientation by Peirce's Pragmatism, and the aim of representing and processing knowledge. These concerns open rich possibilities of interplay and integration. We discuss the philosophical foundations of both disciplines, and analyze their specific qualities. Based on this analysis, we discuss some possible approaches of interplay and integration.

Conceptual knowledge processing with formal concept analysis and ontologies

Among many other knowledge representations formalisms, Ontologies and Formal Concept Analysis (FCA) aim at modeling ‘concepts’. We discuss how these two formalisms may complement another from an application point of view. In particular, we will see how FCA can be used to support Ontology Engineering, and how ontologies can be exploited in FCA applications. The interplay of FCA and ontologies is studied along the life cycle of an ontology: (i) FCA can support the building of the ontology as a learning technique. (ii) The established ontology can be analyzed and navigated by using techniques of FCA. (iii) Last but not least, the ontology may be used to improve an FCA application.

Modeling the interplay between land use, bioenergy production and climate change

Land use has become a force of global importance, considering that 34% of the Earth’s ice-free surface was covered by croplands or pastures in 2000. The expected increase in global human population together with eminent climate change and associated search for energy sources other than fossil fuels can, through land-use and land-cover changes (LUCC), increase the pressure on nature’s resources, further degrade ecosystem services, and disrupt other planetary systems of key importance to humanity. This thesis presents four modeling studies on the interplay between LUCC, increased production of biofuels and climate change in four selected world regions. In the first study case two new crop types (sugarcane and jatropha) are parameterized in the LPJ for managed Lands dynamic global vegetation model for calculation of their potential productivity. Country-wide spatial variation in the yields of sugarcane and jatropha incurs into substantially different land requirements to meet the biofuel production targets for 2015 in Brazil and India, depending on the location of plantations. Particularly the average land requirements for jatropha in India are considerably higher than previously estimated. These findings indicate that crop zoning is important to avoid excessive LUCC. In the second study case the LandSHIFT model of land-use and land-cover changes is combined with life cycle assessments to investigate the occurrence and extent of biofuel-driven indirect land-use changes (ILUC) in Brazil by 2020. The results show that Brazilian biofuels can indeed cause considerable ILUC, especially by pushing the rangeland frontier into the Amazonian forests. The carbon debt caused by such ILUC would result in no carbon savings (from using plant-based ethanol and biodiesel instead of fossil fuels) before 44 years for sugarcane ethanol and 246 years for soybean biodiesel. The intensification of livestock grazing could avoid such ILUC. We argue that such an intensification of livestock should be supported by the Brazilian biofuel sector, based on the sector’s own interest in minimizing carbon emissions. In the third study there is the development of a new method for crop allocation in LandSHIFT, as influenced by the occurrence and capacity of specific infrastructure units. The method is exemplarily applied in a first assessment of the potential availability of land for biogas production in Germany. The results indicate that Germany has enough land to fulfill virtually all (90 to 98%) its current biogas plant capacity with only cultivated feedstocks. Biogas plants located in South and Southwestern (North and Northeastern) Germany might face more (less) difficulties to fulfill their capacities with cultivated feedstocks, considering that feedstock transport distance to plants is a crucial issue for biogas production. In the fourth study an adapted version of LandSHIFT is used to assess the impacts of contrasting scenarios of climate change and conservation targets on land use in the Brazilian Amazon. Model results show that severe climate change in some regions by 2050 can shift the deforestation frontier to areas that would experience low levels of human intervention under mild climate change (such as the western Amazon forests or parts of the Cerrado savannas). Halting deforestation of the Amazon and of the Brazilian Cerrado would require either a reduction in the production of meat or an intensification of livestock grazing in the region. Such findings point out the need for an integrated/multicisciplinary plan for adaptation to climate change in the Amazon. The overall conclusions of this thesis are that (i) biofuels must be analyzed and planned carefully in order to effectively reduce carbon emissions; (ii) climate change can have considerable impacts on the location and extent of LUCC; and (iii) intensification of grazing livestock represents a promising venue for minimizing the impacts of future land-use and land-cover changes in Brazil.

Characterization of DnmA, the Dnmt2 homolog in Dictyostelium discoideum

Eukaryotic DNA m5C methyltransferases (MTases) play a major role in many epigenetic regulatory processes like genomic imprinting, X-chromosome inactivation, silencing of transposons and gene expression. Members of the two DNA m5C MTase families, Dnmt1 and Dnmt3, are relatively well studied and many details of their biological functions, biochemical properties as well as interaction partners are known. In contrast, the biological functions of the highly conserved Dnmt2 family, which appear to have non-canonical dual substrate specificity, remain enigmatic despite the efforts of many researchers. The genome of the social amoeba Dictyostelium encodes Dnmt2-homolog, the DnmA, as the only DNA m5C MTase which allowed us to study Dnmt2 function in this organism without interference by the other enzymes. The dnmA gene can be easily disrupted but the knock-out clones did not show obvious phenotypes under normal lab conditions, suggesting that the function of DnmA is not vital for the organism. It appears that the dnmA gene has a low expression profile during vegetative growth and is only 5-fold upregulated during development. Fluorescence microscopy indicated that DnmA-GFP fusions were distributed between both the nucleus and cytoplasm with some enrichment in nuclei. Interestingly, the experiments showed specific dynamics of DnmA-GFP distribution during the cell cycle. The proteins colocalized with DNA in the interphase and were mainly removed from nuclei during mitosis. DnmA functions as an active DNA m5C MTase in vivo and is responsible for weak but detectable DNA methylation of several regions in the Dictyostelium genome. Nevertheless, gel retardation assays showed only slightly higher affinity of the enzyme to dsDNA compared to ssDNA and no specificity towards various sequence contexts, although weak but detectable specificity towards AT-rich sequences was observed. This could be due to intrinsic curvature of such sequences. Furthermore, DnmA did not show denaturant-resistant covalent complexes with dsDNA in vitro, although it could form covalent adducts with ssDNA. Low binding and methyltransfer activity in vitro suggest the necessity of additional factor in DnmA function. Nevertheless, no candidates could be identified in affinity purification experiments with different tagged DnmA fusions. In this respect, it should be noted that tagged DnmA fusion preparations from Dictyostelium showed somewhat higher activity in both covalent adduct formation and methylation assays than DnmA expressed in E.coli. Thus, the presence of co-purified factors cannot be excluded. The low efficiency of complex formation by the recombinant enzyme and the failure to define interacting proteins that could be required for DNA methylation in vivo, brought up the assumption that post-translational modifications could influence target recognition and enzymatic activity. Indeed, sites of phosphorylation, methylation and acetylation were identified within the target recognition domain (TRD) of DnmA by mass spectrometry. For phosphorylation, the combination of MS data and bioinformatic analysis revealed that some of the sites could well be targets for specific kinases in vivo. Preliminary 3D modeling of DnmA protein based on homology with hDNMT2 allowed us to show that several identified phosphorylation sites located on the surface of the molecule, where they would be available for kinases. The presence of modifications almost solely within the TRD domain of DnmA could potentially modulate the mode of its interaction with the target nucleic acids. DnmA was able to form denaturant-resistant covalent intermediates with several Dictyostelium tRNAs, using as a target C38 in the anticodon loop. The formation of complexes not always correlated with the data from methylation assays, and seemed to be dependent on both sequence and structure of the tRNA substrate. The pattern, previously suggested by the Helm group for optimal methyltransferase activity of hDNMT2, appeared to contribute significantly in the formation of covalent adducts but was not the only feature of the substrate required for DnmA and hDNMT2 functions. Both enzymes required Mg2+ to form covalent complexes, which indicated that the specific structure of the target tRNA was indispensable. The dynamics of covalent adduct accumulation was different for DnmA and different tRNAs. Interestingly, the profiles of covalent adduct accumulation for different tRNAs were somewhat similar for DnmA and hDNMT2 enzymes. According to the proposed catalytic mechanism for DNA m5C MTases, the observed denaturant-resistant complexes corresponded to covalent enamine intermediates. The apparent discrepancies in the data from covalent complex formation and methylation assays may be interpreted by the possibility of alternative pathways of the catalytic mechanism, leading not to methylation but to exchange or demethylation reactions. The reversibility of enamine intermediate formation should also be considered. Curiously, native gel retardation assays showed no or little difference in binding affinities of DnmA to different RNA substrates and thus the absence of specificity in the initial enzyme binding. The meaning of the tRNA methylation as well as identification of novel RNA substrates in vivo should be the aim of further experiments.

Knowledge Building in Landscape Architecture

The objective of this study was to develop an internet-based seminar framework applicable for landscape architecture education. This process was accompanied by various aims. The basic expectation was to keep the main characteristics of landscape architecture education also in the online format. On top of that, four further objectives were anticipated: (1) training of competences for virtual team work, (2) fostering intercultural competence, (3) creation of equal opportunities for education through internet-based open access and (4) synergy effects and learning processes across institutional boundaries. This work started with the hypothesis that these four expected advantages would compensate for additional organisational efforts caused by the online delivery of the seminars and thus lead to a sustainable integration of this new learning mode into landscape architecture curricula. This rationale was followed by a presentation of four areas of knowledge to which the seminar development was directly related (1) landscape architecture as a subject and its pedagogy, (2) general learning theories, (3) developments in the ICT sector and (4) wider societal driving forces such as global citizenship and the increase of open educational resources. The research design took the shape of a pedagogical action research cycle. This approach was constructive: The author herself is teaching international landscape architecture students so that the model could directly be applied in practice. Seven online seminars were implemented in the period from 2008 to 2013 and this experience represents the core of this study. The seminars were conducted with varying themes while its pedagogy, organisation and the technological tools remained widely identical. The research design is further based on three levels of observation: (1) the seminar design on the basis of theory and methods from the learning sciences, in particular educational constructivism, (2) the seminar evaluation and (3) the evaluation of the seminars’ long term impact. The seminar model itself basically consists of four elements: (1) the taxonomy of learning objectives, (2) ICT tools and their application and pedagogy, (3) process models and (4) the case study framework. The seminar framework was followed by the presentation of the evaluation findings. The major findings of this study can be summed up as follows: Implementing online seminars across educational and national boundaries was possible both in term of organisation and technology. In particular, a high level of cultural diversity among the seminar participants has definitively been achieved. However, there were also obvious obstacles. These were primarily competing study commitments and incompatible schedules among the students attending from different academic programmes, partly even in different time zones. Both factors had negative impact on the individual and working group performances. With respect to the technical framework it can be concluded that the majority of the participants were able to use the tools either directly without any problem or after overcoming some smaller problems. Also the seminar wiki was intensively used for completing the seminar assignments. However, too less truly collaborative text production was observed which could be improved by changing the requirements for the collaborative task. Two different process models have been applied for guiding the collaboration of the small groups and both were in general successful. However, it needs to be said that even if the students were able to follow the collaborative task and to co-construct and compare case studies, most of them were not able to synthesize the knowledge they had compiled. This means that the area of consideration often remained on the level of the case and further reflections, generalisations and critique were largely missing. This shows that the seminar model needs to find better ways for triggering knowledge building and critical reflection. It was also suggested to have a more differentiated group building strategy in future seminars. A comparison of pre- and post seminar concept maps showed that an increase of factual and conceptual knowledge on the individual level was widely recognizable. Also the evaluation of the case studies (the major seminar output) revealed that the students have undergone developments of both the factual and the conceptual knowledge domain. Also their self-assessment with respect to individual learning development showed that the highest consensus was achieved in the field of subject-specific knowledge. The participants were much more doubtful with regard to the progress of generic competences such as analysis, communication and organisation. However, 50% of the participants confirmed that they perceived individual development on all competence areas the survey had asked for. Have the additional four targets been met? Concerning the competences for working in a virtual team it can be concluded that the vast majority was able to use the internet-based tools and to work with them in a target-oriented way. However, there were obvious differences regarding the intensity and activity of participation, both because of external and personal factors. A very positive aspect is the achievement of a high cultural diversity supporting the participants’ intercultural competence. Learning from group members was obviously a success factor for the working groups. Regarding the possibilities for better accessibility of educational opportunities it became clear that a significant number of participants were not able to go abroad during their studies because of financial or personal reasons. They confirmed that the online seminar was to some extent a compensation for not having been abroad for studying. Inter-institutional learning and synergy was achieved in so far that many teachers from different countries contributed with individual lectures. However, those teachers hardly ever followed more than one session. Therefore, the learning effect remained largely within the seminar learning group. Looking back at the research design it can be said that the pedagogical action research cycle was an appropriate and valuable approach allowing for strong interaction between theory and practice. However, some more external evaluation from peers in particular regarding the participants’ products would have been valuable.

Atomistic-continuum modeling of ultrafast laser-induced melting of silicon targets

In this work, we present an atomistic-continuum model for simulations of ultrafast laser-induced melting processes in semiconductors on the example of silicon. The kinetics of transient non-equilibrium phase transition mechanisms is addressed with MD method on the atomic level, whereas the laser light absorption, strong generated electron-phonon nonequilibrium, fast heat conduction, and photo-excited free carrier diffusion are accounted for with a continuum TTM-like model (called nTTM). First, we independently consider the applications of nTTM and MD for the description of silicon, and then construct the combined MD-nTTM model. Its development and thorough testing is followed by a comprehensive computational study of fast nonequilibrium processes induced in silicon by an ultrashort laser irradiation. The new model allowed to investigate the effect of laser-induced pressure and temperature of the lattice on the melting kinetics. Two competing melting mechanisms, heterogeneous and homogeneous, were identified in our big-scale simulations. Apart from the classical heterogeneous melting mechanism, the nucleation of the liquid phase homogeneously inside the material significantly contributes to the melting process. The simulations showed, that due to the open diamond structure of the crystal, the laser-generated internal compressive stresses reduce the crystal stability against the homogeneous melting. Consequently, the latter can take a massive character within several picoseconds upon the laser heating. Due to the large negative volume of melting of silicon, the material contracts upon the phase transition, relaxes the compressive stresses, and the subsequent melting proceeds heterogeneously until the excess of thermal energy is consumed. A series of simulations for a range of absorbed fluences allowed us to find the threshold fluence value at which homogeneous liquid nucleation starts contributing to the classical heterogeneous propagation of the solid-liquid interface. A series of simulations for a range of the material thicknesses showed that the sample width we chosen in our simulations (800 nm) corresponds to a thick sample. Additionally, in order to support the main conclusions, the results were verified for a different interatomic potential. Possible improvements of the model to account for nonthermal effects are discussed and certain restrictions on the suitable interatomic potentials are found. As a first step towards the inclusion of these effects into MD-nTTM, we performed nanometer-scale MD simulations with a new interatomic potential, designed to reproduce ab initio calculations at the laser-induced electronic temperature of 18946 K. The simulations demonstrated that, similarly to thermal melting, nonthermal phase transition occurs through nucleation. A series of simulations showed that higher (lower) initial pressure reinforces (hinders) the creation and the growth of nonthermal liquid nuclei. For the example of Si, the laser melting kinetics of semiconductors was found to be noticeably different from that of metals with a face-centered cubic crystal structure. The results of this study, therefore, have important implications for interpretation of experimental data on the kinetics of melting process of semiconductors.