Genometa - A Fast and Accurate Classifier for Short Metagenomic Shotgun Reads

Metagenomic studies use high-throughput sequence data to investigate microbial communities in situ. However, considerable challenges remain in the analysis of these data, particularly with regard to speed and reliable analysis of microbial species as opposed to higher level taxa such as phyla. We here present Genometa, a computationally undemanding graphical user interface program that enables identification of bacterial species and gene content from datasets generated by inexpensive high-throughput short read sequencing technologies. Our approach was first verified on two simulated metagenomic short read datasets, detecting 100% and 94% of the bacterial species included with few false positives or false negatives. Subsequent comparative benchmarking analysis against three popular metagenomic algorithms on an Illumina human gut dataset revealed Genometa to attribute the most reads to bacteria at species level (i.e. including all strains of that species) and demonstrate similar or better accuracy than the other programs. Lastly, speed was demonstrated to be many times that of BLAST due to the use of modern short read aligners. Our method is highly accurate if bacteria in the sample are represented by genomes in the reference sequence but cannot find species absent from the reference. This method is one of the most user-friendly and resource efficient approaches and is thus feasible for rapidly analysing millions of short reads on a personal computer.

A matlab-based toolbox for the simulation and design of L1 adaptive controllers

This thesis introduces the L1 Adaptive Control Toolbox, a set of tools implemented in Matlab that aid in the design process of an L1 adaptive controller and enable the user to construct simulations of the closed-loop system to verify its performance. Following a brief review of the existing theory on L1 adaptive controllers, the interface of the toolbox is presented, including a description of the functions accessible to the user. Two novel algorithms for determining the required sampling period of a piecewise constant adaptive law are presented and their implementation in the toolbox is discussed. The detailed description of the structure of the toolbox is provided as well as a discussion of the implementation of the creation of simulations. Finally, the graphical user interface is presented and described in detail, including the graphical design tools provided for the development of the filter C(s). The thesis closes with suggestions for further improvement of the toolbox.

Online MBPeT dashboard : enabling performance testing as a service in the cloud

In this thesis, tool support is addressed for the combined disciplines of Model-based testing and performance testing. Model-based testing (MBT) utilizes abstract behavioral models to automate test generation, thus decreasing time and cost of test creation. MBT is a functional testing technique, thereby focusing on output, behavior, and functionality. Performance testing, however, is non-functional and is concerned with responsiveness and stability under various load conditions. MBPeT (Model-Based Performance evaluation Tool) is one such tool which utilizes probabilistic models, representing dynamic real-world user behavior patterns, to generate synthetic workload against a System Under Test and in turn carry out performance analysis based on key performance indicators (KPI). Developed at Åbo Akademi University, the MBPeT tool is currently comprised of a downloadable command-line based tool as well as a graphical user interface. The goal of this thesis project is two-fold: 1) to extend the existing MBPeT tool by deploying it as a web-based application, thereby removing the requirement of local installation, and 2) to design a user interface for this web application which will add new user interaction paradigms to the existing feature set of the tool. All phases of the MBPeT process will be realized via this single web deployment location including probabilistic model creation, test configurations, test session execution against a SUT with real-time monitoring of user configurable metric, and final test report generation and display. This web application (MBPeT Dashboard) is implemented with the Java programming language on top of the Vaadin framework for rich internet application development. The Vaadin framework handles the complicated web communications processes and front-end technologies, freeing developers to implement the business logic as well as the user interface in pure Java. A number of experiments are run in a case study environment to validate the functionality of the newly developed Dashboard application as well as the scalability of the solution implemented in handling multiple concurrent users. The results support a successful solution with regards to the functional and performance criteria defined, while improvements and optimizations are suggested to increase both of these factors.

Event-Code Interaction Directed Test Cases

The Graphical User Interface (GUI) is an integral component of contemporary computer software. A stable and reliable GUI is necessary for correct functioning of software applications. Comprehensive verification of the GUI is a routine part of most software development life-cycles. The input space of a GUI is typically large, making exhaustive verification difficult. GUI defects are often revealed by exercising parts of the GUI that interact with each other. It is challenging for a verification method to drive the GUI into states that might contain defects. In recent years, model-based methods, that target specific GUI interactions, have been developed. These methods create a formal model of the GUI’s input space from specification of the GUI, visible GUI behaviors and static analysis of the GUI’s program-code. GUIs are typically dynamic in nature, whose user-visible state is guided by underlying program-code and dynamic program-state. This research extends existing model-based GUI testing techniques by modelling interactions between the visible GUI of a GUI-based software and its underlying program-code. The new model is able to, efficiently and effectively, test the GUI in ways that were not possible using existing methods. The thesis is this: Long, useful GUI testcases can be created by examining the interactions between the GUI, of a GUI-based application, and its program-code. To explore this thesis, a model-based GUI testing approach is formulated and evaluated. In this approach, program-code level interactions between GUI event handlers will be examined, modelled and deployed for constructing long GUI testcases. These testcases are able to drive the GUI into states that were not possible using existing models. Implementation and evaluation has been conducted using GUITAR, a fully-automated, open-source GUI testing framework.

Plataforma interactiva para edifícios inteligentes com controlo preditivo

Esta dissertação desenvolve uma plataforma de controlo interactiva para edifícios inteligentes através de um sistema SCADA (Supervisory Control And Data Acquisition). Este sistema SCADA integra diferentes tipos de informações provenientes das várias tecnologias presentes em edifícios modernos (controlo da ventilação, temperatura, iluminação, etc.). A estratégia de controlo desenvolvida implementa um controlador em cascada hierárquica onde os "loops" interiores são executados pelos PLC's locais (Programmable Logic Controller), e o "loop" exterior é gerido pelo sistema SCADA centralizado, que interage com a rede local de PLC's. Nesta dissertação é implementado um controlador preditivo na plataforma SCADA centralizada. São apresentados testes efectuados para o controlo da temperatura e luminosidade de salas com uma grande área. O controlador preditivo desenvolvido tenta optimizar a satisfação dos utilizadores, com base nas preferências introduzidas em várias interfaces distribuídas, sujeito às restrições de minimização do desperdício de energia. De forma a executar o controlador preditivo na plataforma SCADA foi desenvolvido um canal de comunicação para permitir a comunicação entre a aplicação SCADA e a aplicação MATLAB, onde o controlador preditivo é executado. ABSTRACT: This dissertation develops an operational control platform for intelligent buildings using a SCADA system (Supervisory Control And Data Acquisition). This SCADA system integrates different types of information coming from the several technologies present in modem buildings (control of ventilation, temperature, illumination, etc.). The developed control strategy implements a hierarchical cascade controller where inner loops are performed by local PLCs (Programmable Logic Controller), and the outer loop is managed by the centralized SCADA system, which interacts with the entire local PLC network. ln this dissertation a Predictive Controller is implemented at the centralized SCADA platform. Tests applied to the control of temperature and luminosity in huge­area rooms are presented. The developed Predictive Controller tries to optimize the satisfaction of user explicit preferences coming from several distributed user-interfaces, subjected to the constraints of energy waste minimization. ln order to run the Predictive Controller at the SCADA platform a communication channel was developed to allow communication between the SCADA application and the MATLAB application where the Predictive Controller runs.

Falcon herramientas de software para el procesamiento aerofotogramétrico

En el área de Aerofotogrametría Digital, el software comercial prevalente para postproceso presenta limitaciones debido a dos factores: (i) las legislaciones de cada país o región requieren diferentes convenciones, y (ii) las necesidades de las empresas son tan cambiantes que no justifican la compra de software de alto rendimiento, que puede quedar sin utilizar debido a un viraje del mercado -- El presente proyecto se ha desarrollado para atender necesidades de procesamiento automático de planos (partición, detección y corrección de errores, etc.), así como módulos de importación – exportación paquete a paquete, trazado de rutas e interacción con GPS -- Este artículo informa de los dos últimos aspectos -- Debido a necesidades de los clientes, los archivos entregados deben llevar un formato comercial (DWG, DXF), pero el procesamiento de los archivos debe ser hecho en paquetes y formatos diversos (DGN) -- Por lo tanto, fue necesario diseñar e implementar un formato acompañante que permitió llevar la información que se pierde al usar filtros comerciales (DGN a DXF/DWG) -- Asimismo se crearon módulos de importación y exportación redundantes, que hicieron efectivos dichos atributos -- En el aspecto de generación de rutas de vuelo, se reportan en este artículo la aplicación de algoritmos tradicionales de barrido (peinado) de áreas 2D, a los cuales se agregaron restricciones geométricas (puntos fijos, offsets, orden de los barridos de acuerdo a coordenadas del sitio de partida, etc.) -- Debido a los altos costos de equipos equivalentes, se decidió desarrollar software para traducción de rutas entre formatos GPS y formatos geográficos locales al país -- Ello permite la eliminación de fuentes de error y además facilita la carga del plan de vuelo, a costos mucho menores a los del hardware / software comercial

Compressão de Imagens Usando a Função de Peano e a Transformada Wavelet 1D

In this work, spoke about the importance of image compression for the industry, it is known that processing and image storage is always a challenge in petrobrás to optimize the storage time and store a maximum number of images and data. We present an interactive system for processing and storing images in the wavelet domain and an interface for digital image processing. The proposal is based on the Peano function and wavelet transform in 1D. The storage system aims to optimize the computational space, both for storage and for transmission of images. Being necessary to the application of the Peano function to linearize the images and the 1D wavelet transform to decompose it. These applications allow you to extract relevant information for the storage of an image with a lower computational cost and with a very small margin of error when comparing the images, original and processed, ie, there is little loss of quality when applying the processing system presented . The results obtained from the information extracted from the images are displayed in a graphical interface. It is through the graphical user interface that the user uses the files to view and analyze the results of the programs directly on the computer screen without the worry of dealing with the source code. The graphical user interface, programs for image processing via Peano Function and Wavelet Transform 1D, were developed in Java language, allowing a direct exchange of information between them and the user

INTEGRATION OF INSTRUMENTATION AND PROCESSING SOFTWARE OF A LASER SPECKLE CONTRAST IMAGING SYSTEM

Laser speckle contrast imaging (LSCI) has the potential to be a powerful tool in medicine, but more research in the field is required so it can be used properly. To help in the progression of Michigan Tech's research in the field, a graphical user interface (GUI) was designed in Matlab to control the instrumentation of the experiments as well as process the raw speckle images into contrast images while they are being acquired. The design of the system was successful and is currently being used by Michigan Tech's Biomedical Engineering department. This thesis describes the development of the LSCI GUI as well as offering a full introduction into the history, theory and applications of LSCI.

DEVELOPMENT OF ION EXCHANGE MODELS FOR WATER TREATMENT AND APPLICATION TO THE INTERNATIONAL SPACE STATION WATER PROCESSOR

The International Space Station (ISS) requires a substantial amount of potable water for use by the crew. The economic and logistic limitations of transporting the vast amount of water required onboard the ISS necessitate onboard recovery and reuse of the aqueous waste streams. Various treatment technologies are employed within the ISS water processor to render the waste water potable, including filtration, ion exchange, adsorption, and catalytic wet oxidation. The ion exchange resins and adsorption media are combined in multifiltration beds for removal of ionic and organic compounds. A mathematical model (MFBMODEL™) designed to predict the performance of a multifiltration (MF) bed was developed. MFBMODEL consists of ion exchange models for describing the behavior of the different resin types in a MF bed (e.g., mixed bed, strong acid cation, strong base anion, and weak base anion exchange resins) and an adsorption model capable of predicting the performance of the adsorbents in a MF bed. Multicomponent ion exchange ii equilibrium models that incorporate the water formation reaction, electroneutrality condition, and degree of ionization of weak acids and bases for mixed bed, strong acid cation, strong base anion, and weak base anion exchange resins were developed and verified. The equilibrium models developed use a tanks-inseries approach that allows for consideration of variable influent concentrations. The adsorption modeling approach was developed in related studies and application within the MFBMODEL framework was demonstrated in the Appendix to this study. MFBMODEL consists of a graphical user interface programmed in Visual Basic and Fortran computational routines. This dissertation shows MF bed modeling results in which the model is verified for a surrogate of the ISS waste shower and handwash stream. In addition, a multicomponent ion exchange model that incorporates mass transfer effects was developed, which is capable of describing the performance of strong acid cation (SAC) and strong base anion (SBA) exchange resins, but not including reaction effects. This dissertation presents results showing the mass transfer model's capability to predict the performance of binary and multicomponent column data for SAC and SBA exchange resins. The ion exchange equilibrium and mass transfer models developed in this study are also applicable to terrestrial water treatment systems. They could be applied for removal of cations and anions from groundwater (e.g., hardness, nitrate, perchlorate) and from industrial process waters (e.g. boiler water, ultrapure water in the semiconductor industry).

Predicting the concentration of residual methanol in industrial formalin using machine learning

In this thesis, a machine learning approach was used to develop a predictive model for residual methanol concentration in industrial formalin produced at the Akzo Nobel factory in Kristinehamn, Sweden. The MATLABTM computational environment supplemented with the Statistics and Machine LearningTM toolbox from the MathWorks were used to test various machine learning algorithms on the formalin production data from Akzo Nobel. As a result, the Gaussian Process Regression algorithm was found to provide the best results and was used to create the predictive model. The model was compiled to a stand-alone application with a graphical user interface using the MATLAB CompilerTM.

1H NMR Relaxation Characterization Of Hydrates

To distinguish the components of NMR signals from hydrated materials and to monitor their evolution after the addition of water to the powders, during the first two days of hydration. To implement the 3 Tau Model in a MATLAB script, called 3TM, provided with a Graphical User Interface (GUI), to easily use the 3 Tau Model with NMRD profiles. The 3 Tau Model, developed a few years ago is used for interpreting the dispersion (NMRD profiles, dependence on the Larmor frequency) of the longitudinal relaxation times, for liquids confined in porous media. This model describes the molecular dynamics of confined molecules by introducing three characteristic correlation times and additional outputs.

Machine Learning algorithm on seat comfort level measurement, mapping pressure values with body regions

The comfort level of the seat has a major effect on the usage of a vehicle; thus, car manufacturers have been working on elevating car seat comfort as much as possible. However, still, the testing and evaluation of comfort are done using exhaustive trial and error testing and evaluation of data. In this thesis, we resort to machine learning and Artificial Neural Networks (ANN) to develop a fully automated approach. Even though this approach has its advantages in minimizing time and using a large set of data, it takes away the degree of freedom of the engineer on making decisions. The focus of this study is on filling the gap in a two-step comfort level evaluation which used pressure mapping with body regions to evaluate the average pressure supported by specific body parts and the Self-Assessment Exam (SAE) questions on evaluation of the person’s interest. This study has created a machine learning algorithm that works on giving a degree of freedom to the engineer in making a decision when mapping pressure values with body regions using ANN. The mapping is done with 92% accuracy and with the help of a Graphical User Interface (GUI) that facilitates the process during the testing time of comfort level evaluation of the car seat, which decreases the duration of the test analysis from days to hours.

Sviluppo di un modello previsionale del comportamento magnetico di leghe Fe-Si

Il presente lavoro di tesi ha lo scopo di implementare un modello previsionale del comportamento magnetico di leghe Fe-Si in regime statico e dinamico, mediante l’identificazione e l’ottimizzazione dei parametri caratteristici del modello di Jiles-Atherton. Tale fine è stato perseguito attraverso l’uso del software di calcolo Matlab-Simulink. Il modello, validato mediante i dati reperibili in letteratura, permette di simulare la curva di prima magnetizzazione e il ciclo di isteresi per materiali ferromagnetici soft mediante la conoscenza di un set limitato di dati sperimentali ricavabili dalle prove magnetiche. Il modello è stato impiegato per eseguire la simulazione anche su campioni prodotti industrialmente in acciaio al silicio a grano non orientato forniti allo stato fully-processed M470-50A preventivamente sottoposti a caratterizzazione microstrutturale, mediante microscopia ottica, elettronica e analisi EBSD, e meccanica, attraverso le prove di trazione. I risultati ottenuti dalla simulazione presentano ottimale accuratezza, in particolar modo nel caso statico sia in termini di estrazione dei parametri sia di definizione del ciclo; risulta ancora da migliorare ulteriormente il grafico in frequenza. Al fine di rendere fruibile il modello realizzato è stata progettata una Graphical User Interface. Nell’ottica di una mobilità green in accordo con gli obiettivi globali, l’implementazione del presente modello pone quindi le basi per uno studio futuro del comportamento dei materiali magnetici per la realizzazione di motori elettrici sempre più performanti in funzione dei parametri di produzione e delle condizioni di utilizzo, aspetti che incidono notevolmente sulle proprietà di tale materiale.

Construção de interfaces em Flex para sistemas de experimentação remota

Os laboratórios de experimentação remota estão normalmente associados a tecnologias ou soluções proprietárias, as quais restringem a sua utilização a determinadas plataformas e obrigam ao uso de software específico no lado do cliente. O ISEP possui um laboratório de experimentação remota, baseado em instrumentação virtual, usado no apoio ao ensino da electrónica e construído sobre uma plataforma NIELVIS da National Instruments. O software de controlo da plataforma recorre à linguagem gráfica de programação LabVIEW. Esta é uma ferramenta desenvolvida pela National Instruments que facilita o desenvolvimento de aplicações de sistemas de experimentação remota, mas que possui várias limitações, nomeadamente a necessidade de instalação do lado do cliente de um plug-in, cuja disponibilidade se encontra limitada a determinadas versões de sistemas operativos e de Web Browsers. A experiência anterior demonstrou que estas questões limitam o número de clientes com possibilidade de acesso ao laboratório remoto, para além de, em alguns casos, se ter verificado não ser transparente a sua instalação e utilização. Neste contexto, o trabalho de investigação consistiu no desenvolvimento de uma solução que permite a geração de interfaces que possibilitam o controlo remoto do sistema implementado, e que, ao mesmo tempo, são independentes da plataforma usada pelo cliente.