Implementation of Quantitative Reaction-based Model Refinement

Building a computational model for complex biological systems is an iterative process. It starts from an abstraction of the process and then incorporates more details regarding the specific biochemical reactions which results in the change of the model fit. Meanwhile, the model’s numerical properties such as its numerical fit and validation should be preserved. However, refitting the model after each refinement iteration is computationally expensive resource-wise. There is an alternative approach which ensures the model fit preservation without the need to refit the model after each refinement iteration. And this approach is known as quantitative model refinement. The aim of this thesis is to develop and implement a tool called ModelRef which does the quantitative model refinement automatically. It is both implemented as a stand-alone Java application and as one of Anduril framework components. ModelRef performs data refinement of a model and generates the results in two different well known formats (SBML and CPS formats). The development of this tool successfully reduces the time and resource needed and the errors generated as well by traditional reiteration of the whole model to perform the fitting procedure.

Lean management implementation in Horizontal Technology Transfer projects

The importance of Technology Transfer activities of companies is underpinned by the changes in technological and economic environments. However, there is still a significant gap in defining possible ways for Technology Transfer projects effectiveness improvement. The Master’s Thesis overviews common problems faced by the companies in implementation of Technology Transfer projects and examines Lean management principles as possible way to improve its effectiveness. Based on the analysis of the relevant scientific literature and results of the survey, conducted among the firms of different types, the approach to Technology Transfer projects implementation with the use of Lean management principles is proposed. The approach serves to solve some of the important problems faced by the managers of Technology Transfer projects. It is envisaged that this approach can help to increase overall Technology Transfer projects’ effectiveness.

Design and implementation of machine vision system for the mobile assembly robot

The review of intelligent machines shows that the demand for new ways of helping people in perception of the real world is becoming higher and higher every year. This thesis provides information about design and implementation of machine vision for mobile assembly robot. The work has been done as a part of LUT project in Laboratory of Intelligent Machines. The aim of this work is to create a working vision system. The qualitative and quantitative research were done to complete this task. In the first part, the author presents the theoretical background of such things as digital camera work principles, wireless transmission basics, creation of live stream, methods used for pattern recognition. Formulas, dependencies and previous research related to the topic are shown. In the second part, the equipment used for the project is described. There is information about the brands, models, capabilities and also requirements needed for implementation. Although, the author gives a description of LabVIEW software, its add-ons and OpenCV which are used in the project. Furthermore, one can find results in further section of considered thesis. They mainly represented by screenshots from cameras, working station and photos of the system. The key result of this thesis is vision system created for the needs of mobile assembly robot. Therefore, it is possible to see graphically what was done on examples. Future research in this field includes optimization of the pattern recognition algorithm. This will give less response time for recognizing objects. Presented by author system can be used also for further activities which include artificial intelligence usage.

A System for Models of First Order Theories

If you want to know whether a property is true or not in a specific algebraic structure,you need to test that property on the given structure. This can be done by hand, which can be cumbersome and erroneous. In addition, the time consumed in testing depends on the size of the structure where the property is applied. We present an implementation of a system for finding counterexamples and testing properties of models of first-order theories. This system is supposed to provide a convenient and paperless environment for researchers and students investigating or studying such models and algebraic structures in particular. To implement a first-order theory in the system, a suitable first-order language.( and some axioms are required. The components of a language are given by a collection of variables, a set of predicate symbols, and a set of operation symbols. Variables and operation symbols are used to build terms. Terms, predicate symbols, and the usual logical connectives are used to build formulas. A first-order theory now consists of a language together with a set of closed formulas, i.e. formulas without free occurrences of variables. The set of formulas is also called the axioms of the theory. The system uses several different formats to allow the user to specify languages, to define axioms and theories and to create models. Besides the obvious operations and tests on these structures, we have introduced the notion of a functor between classes of models in order to generate more co~plex models from given ones automatically. As an example, we will use the system to create several lattices structures starting from a model of the theory of pre-orders.

Speaker identification using models for phonemes

Motivation for Speaker recognition work is presented in the first part of the thesis. An exhaustive survey of past work in this field is also presented. A low cost system not including complex computation has been chosen for implementation. Towards achieving this a PC based system is designed and developed. A front end analog to digital convertor (12 bit) is built and interfaced to a PC. Software to control the ADC and to perform various analytical functions including feature vector evaluation is developed. It is shown that a fixed set of phrases incorporating evenly balanced phonemes is aptly suited for the speaker recognition work at hand. A set of phrases are chosen for recognition. Two new methods are adopted for the feature evaluation. Some new measurements involving a symmetry check method for pitch period detection and ACE‘ are used as featured. Arguments are provided to show the need for a new model for speech production. Starting from heuristic, a knowledge based (KB) speech production model is presented. In this model, a KB provides impulses to a voice producing mechanism and constant correction is applied via a feedback path. It is this correction that differs from speaker to speaker. Methods of defining measurable parameters for use as features are described. Algorithms for speaker recognition are developed and implemented. Two methods are presented. The first is based on the model postulated. Here the entropy on the utterance of a phoneme is evaluated. The transitions of voiced regions are used as speaker dependent features. The second method presented uses features found in other works, but evaluated differently. A knock—out scheme is used to provide the weightage values for the selection of features. Results of implementation are presented which show on an average of 80% recognition. It is also shown that if there are long gaps between sessions, the performance deteriorates and is speaker dependent. Cross recognition percentages are also presented and this in the worst case rises to 30% while the best case is 0%. Suggestions for further work are given in the concluding chapter.

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. -----------------------------------------------------------------------

Transition between metadata models: approach based on the use open source software

This article shows the work developed for adapting metadata conform to the official Colombian metadata standard NTC 4611 to the international standard ISO 19115. CatMDedit, an open source metadata editor, is used in this task. CatMDedit is able of import variants of CSDGM such as NTC 4611 and export to the stable version of ISO 19139 (the XML implementation model of ISO 19115)

Development, implementation and evaluation of an activated sludge supervisory system for the Granollers WWTP

La present tesi pretén recollir l'experiència viscuda en desenvolupar un sistema supervisor intel·ligent per a la millora de la gestió de plantes depuradores d'aigües residuals., implementar-lo en planta real (EDAR Granollers) i avaluar-ne el funcionament dia a dia amb situacions típiques de la planta. Aquest sistema supervisor combina i integra eines de control clàssic de les plantes depuradores (controlador automàtic del nivell d'oxigen dissolt al reactor biològic, ús de models descriptius del procés...) amb l'aplicació d'eines del camp de la intel·ligència artificial (sistemes basats en el coneixement, concretament sistemes experts i sistemes basats en casos, i xarxes neuronals). Aquest document s'estructura en 9 capítols diferents. Hi ha una primera part introductòria on es fa una revisió de l'estat actual del control de les EDARs i s'explica el perquè de la complexitat de la gestió d'aquests processos (capítol 1). Aquest capítol introductori juntament amb el capítol 2, on es pretén explicar els antecedents d'aquesta tesi, serveixen per establir els objectius d'aquest treball (capítol 3). A continuació, el capítol 4 descriu les peculiaritats i especificitats de la planta que s'ha escollit per implementar el sistema supervisor. Els capítols 5 i 6 del present document exposen el treball fet per a desenvolupar el sistema basat en regles o sistema expert (capítol 6) i el sistema basat en casos (capítol 7). El capítol 8 descriu la integració d'aquestes dues eines de raonament en una arquitectura multi nivell distribuïda. Finalment, hi ha una darrer capítol que correspon a la avaluació (verificació i validació), en primer lloc, de cadascuna de les eines per separat i, posteriorment, del sistema global en front de situacions reals que es donin a la depuradora

Calibration of uncertain flood inundation models using remotely sensed water levels

A traditional method of validating the performance of a flood model when remotely sensed data of the flood extent are available is to compare the predicted flood extent to that observed. The performance measure employed often uses areal pattern-matching to assess the degree to which the two extents overlap. Recently, remote sensing of flood extents using synthetic aperture radar (SAR) and airborne scanning laser altimetry (LIDAR) has made more straightforward the synoptic measurement of water surface elevations along flood waterlines, and this has emphasised the possibility of using alternative performance measures based on height. This paper considers the advantages that can accrue from using a performance measure based on waterline elevations rather than one based on areal patterns of wet and dry pixels. The two measures were compared for their ability to estimate flood inundation uncertainty maps from a set of model runs carried out to span the acceptable model parameter range in a GLUE-based analysis. A 1 in 5-year flood on the Thames in 1992 was used as a test event. As is typical for UK floods, only a single SAR image of observed flood extent was available for model calibration and validation. A simple implementation of a two-dimensional flood model (LISFLOOD-FP) was used to generate model flood extents for comparison with that observed. The performance measure based on height differences of corresponding points along the observed and modelled waterlines was found to be significantly more sensitive to the channel friction parameter than the measure based on areal patterns of flood extent. The former was able to restrict the parameter range of acceptable model runs and hence reduce the number of runs necessary to generate an inundation uncertainty map. A result of this was that there was less uncertainty in the final flood risk map. The uncertainty analysis included the effects of uncertainties in the observed flood extent as well as in model parameters. The height-based measure was found to be more sensitive when increased heighting accuracy was achieved by requiring that observed waterline heights varied slowly along the reach. The technique allows for the decomposition of the reach into sections, with different effective channel friction parameters used in different sections, which in this case resulted in lower r.m.s. height differences between observed and modelled waterlines than those achieved by runs using a single friction parameter for the whole reach. However, a validation of the modelled inundation uncertainty using the calibration event showed a significant difference between the uncertainty map and the observed flood extent. While this was true for both measures, the difference was especially significant for the height-based one. This is likely to be due to the conceptually simple flood inundation model and the coarse application resolution employed in this case. The increased sensitivity of the height-based measure may lead to an increased onus being placed on the model developer in the production of a valid model

Fitting models for the joint action of two drugs using SAS(R)

Combinations of drugs are increasingly being used for a wide variety of diseases and conditions. A pre-clinical study may allow the investigation of the response at a large number of dose combinations. In determining the response to a drug combination, interest may lie in seeking evidence of synergism, in which the joint action is greater than the actions of the individual drugs, or of antagonism, in which it is less. Two well-known response surface models representing no interaction are Loewe additivity and Bliss independence, and Loewe or Bliss synergism or antagonism is defined relative to these. We illustrate an approach to fitting these models for the case in which the marginal single drug dose-response relationships are represented by four-parameter logistic curves with common upper and lower limits, and where the response variable is normally distributed with a common variance about the dose-response curve. When the dose-response curves are not parallel, the relative potency of the two drugs varies according to the magnitude of the desired effect and the models for Loewe additivity and synergism/antagonism cannot be explicitly expressed. We present an iterative approach to fitting these models without the assumption of parallel dose-response curves. A goodness-of-fit test based on residuals is also described. Implementation using the SAS NLIN procedure is illustrated using data from a pre-clinical study. Copyright © 2007 John Wiley & Sons, Ltd.

Demographic models and the management of endangered species: a case study of the critically endangered Seychelles magpie robin

1. Demographic models are assuming an important role in management decisions for endangered species. Elasticity analysis and scope for management analysis are two such applications. Elasticity analysis determines the vital rates that have the greatest impact on population growth. Scope for management analysis examines the effects that feasible management might have on vital rates and population growth. Both methods target management in an attempt to maximize population growth. 2. The Seychelles magpie robin Copsychus sechellarum is a critically endangered island endemic, the population of which underwent significant growth in the early 1990s following the implementation of a recovery programme. We examined how the formal use of elasticity and scope for management analyses might have shaped management in the recovery programme, and assessed their effectiveness by comparison with the actual population growth achieved. 3. The magpie robin population doubled from about 25 birds in 1990 to more than 50 by 1995. A simple two-stage demographic model showed that this growth was driven primarily by a significant increase in the annual survival probability of first-year birds and an increase in the birth rate. Neither the annual survival probability of adults nor the probability of a female breeding at age 1 changed significantly over time. 4. Elasticity analysis showed that the annual survival probability of adults had the greatest impact on population growth. There was some scope to use management to increase survival, but because survival rates were already high (> 0.9) this had a negligible effect on population growth. Scope for management analysis showed that significant population growth could have been achieved by targeting management measures at the birth rate and survival probability of first-year birds, although predicted growth rates were lower than those achieved by the recovery programme when all management measures were in place (i.e. 1992-95). 5. Synthesis and applications. We argue that scope for management analysis can provide a useful basis for management but will inevitably be limited to some extent by a lack of data, as our study shows. This means that identifying perceived ecological problems and designing management to alleviate them must be an important component of endangered species management. The corollary of this is that it will not be possible or wise to consider only management options for which there is a demonstrable ecological benefit. Given these constraints, we see little role for elasticity analysis because, when data are available, a scope for management analysis will always be of greater practical value and, when data are lacking, precautionary management demands that as many perceived ecological problems as possible are tackled.

SORMA - business cases for an open grid market: concept and implementation

Economic mechanisms enhance technological solutions by setting the right incentives to reveal information about demand and supply accurately. Market or pricing mechanisms are ones that foster information exchange and can therefore attain efficient allocation. By assigning a value (also called utility) to their service requests, users can reveal their relative urgency or costs to the service. The implementation of theoretical sound models induce further complex challenges. The EU-funded project SORMA analyzes these challenges and provides a prototype as a proof-of-concept. In this paper the approach within the SORMA-project is described on both conceptual and technical level.

Parallel implementation and one year experiments with the Danish Eulerian Model

Large scale air pollution models are powerful tools, designed to meet the increasing demand in different environmental studies. The atmosphere is the most dynamic component of the environment, where the pollutants can be moved quickly on far distnce. Therefore the air pollution modeling must be done in a large computational domain. Moreover, all relevant physical, chemical and photochemical processes must be taken into account. In such complex models operator splitting is very often applied in order to achieve sufficient accuracy as well as efficiency of the numerical solution. The Danish Eulerian Model (DEM) is one of the most advanced such models. Its space domain (4800 × 4800 km) covers Europe, most of the Mediterian and neighboring parts of Asia and the Atlantic Ocean. Efficient parallelization is crucial for the performance and practical capabilities of this huge computational model. Different splitting schemes, based on the main processes mentioned above, have been implemented and tested with respect to accuracy and performance in the new version of DEM. Some numerical results of these experiments are presented in this paper.

A mathematical model, implementation and study of a swarm system

The work reported in this paper is motivated towards the development of a mathematical model for swarm systems based on macroscopic primitives. A pattern formation and transformation model is proposed. The pattern transformation model comprises two general methods for pattern transformation, namely a macroscopic transformation method and a mathematical transformation method. The problem of transformation is formally expressed and four special cases of transformation are considered. Simulations to confirm the feasibility of the proposed models and transformation methods are presented. Comparison between the two transformation methods is also reported.

Comparing tube models for predicting the linear rheology of branched polymer melts

The hierarchical and "bob" (or branch-on-branch) models are tube-based computational models recently developed for predicting the linear rheology of general mixtures of polydisperse branched polymers. These two models are based on a similar tube-theory framework but differ in their numerical implementation and details of relaxation mechanisms. We present a detailed overview of the similarities and differences of these models and examine the effects of these differences on the predictions of the linear viscoelastic properties of a set of representative branched polymer samples in order to give a general picture of the performance of these models. Our analysis confirms that the hierarchical and bob models quantitatively predict the linear rheology of a wide range of branched polymer melts but also indicate that there is still no unique solution to cover all types of branched polymers without case-by-case adjustment of parameters such as the dilution exponent alpha and the factor p(2) which defines the hopping distance of a branch point relative to the tube diameter. An updated version of the hierarchical model, which shows improved computational efficiency and refined relaxation mechanisms, is introduced and used in these analyses.