Algorithmen zur labelfreien quantitativen Proteomanalyse auf Basis datenunabhängig-akquirierter LC-MS-Daten

Moderne ESI-LC-MS/MS-Techniken erlauben in Verbindung mit Bottom-up-Ansätzen eine qualitative und quantitative Charakterisierung mehrerer tausend Proteine in einem einzigen Experiment. Für die labelfreie Proteinquantifizierung eignen sich besonders datenunabhängige Akquisitionsmethoden wie MSE und die IMS-Varianten HDMSE und UDMSE. Durch ihre hohe Komplexität stellen die so erfassten Daten besondere Anforderungen an die Analysesoftware. Eine quantitative Analyse der MSE/HDMSE/UDMSE-Daten blieb bislang wenigen kommerziellen Lösungen vorbehalten. rn| In der vorliegenden Arbeit wurden eine Strategie und eine Reihe neuer Methoden zur messungsübergreifenden, quantitativen Analyse labelfreier MSE/HDMSE/UDMSE-Daten entwickelt und als Software ISOQuant implementiert. Für die ersten Schritte der Datenanalyse (Featuredetektion, Peptid- und Proteinidentifikation) wird die kommerzielle Software PLGS verwendet. Anschließend werden die unabhängigen PLGS-Ergebnisse aller Messungen eines Experiments in einer relationalen Datenbank zusammengeführt und mit Hilfe der dedizierten Algorithmen (Retentionszeitalignment, Feature-Clustering, multidimensionale Normalisierung der Intensitäten, mehrstufige Datenfilterung, Proteininferenz, Umverteilung der Intensitäten geteilter Peptide, Proteinquantifizierung) überarbeitet. Durch diese Nachbearbeitung wird die Reproduzierbarkeit der qualitativen und quantitativen Ergebnisse signifikant gesteigert.rn| Um die Performance der quantitativen Datenanalyse zu evaluieren und mit anderen Lösungen zu vergleichen, wurde ein Satz von exakt definierten Hybridproteom-Proben entwickelt. Die Proben wurden mit den Methoden MSE und UDMSE erfasst, mit Progenesis QIP, synapter und ISOQuant analysiert und verglichen. Im Gegensatz zu synapter und Progenesis QIP konnte ISOQuant sowohl eine hohe Reproduzierbarkeit der Proteinidentifikation als auch eine hohe Präzision und Richtigkeit der Proteinquantifizierung erreichen.rn| Schlussfolgernd ermöglichen die vorgestellten Algorithmen und der Analyseworkflow zuverlässige und reproduzierbare quantitative Datenanalysen. Mit der Software ISOQuant wurde ein einfaches und effizientes Werkzeug für routinemäßige Hochdurchsatzanalysen labelfreier MSE/HDMSE/UDMSE-Daten entwickelt. Mit den Hybridproteom-Proben und den Bewertungsmetriken wurde ein umfassendes System zur Evaluierung quantitativer Akquisitions- und Datenanalysesysteme vorgestellt.

Compensability index for compensation radiotherapy after treatment interruptions

Background The goal of our work was to develop a simple method to evaluate a compensation treatment after unplanned treatment interruptions with respect to their tumour- and normal tissue effect. Methods We developed a software tool in java programming language based on existing recommendations to compensate for treatment interruptions. In order to express and visualize the deviations from the originally planned tumour and normal tissue effects we defined the compensability index. Results The compensability index represents an evaluation of the suitability of compensatory radiotherapy in a single number based on the number of days used for compensation and the preference of preserving the originally planned tumour effect or not exceeding the originally planned normal tissue effect. An automated tool provides a method for quick evaluation of compensation treatments. Conclusions The compensability index calculation may serve as a decision support system based on existing and established recommendations.

Estudio preliminar acerca del uso de protocolos y actos comunicativos FIPA en el sistema COMPUTAPLEX

Este trabajo corresponde con la implementación de componentes software dentro de la Plataforma COMPUTAPLEX, la cual tiene como objetivo facilitar a los investigadores la realización de tareas del proceso experimental de ingeniería de software. Uno de los aportes a esta plataforma tecnológica corresponde con el desarrolló de los componentes necesarios para la recuperación de datos experimentales disponibles en diversas fuentes de datos, para ello se hizo uso de un mecanismo capaz de unificar la extracción de información de MySQL, ficheros excel y ficheros SPSS. Con ello diferentes grupos de investigación asociados pueden compartir y tener acceso a repositorios experimentales que se mantienen tanto de manera local como externa. Por otra parte, se ha realizado un estudio de la tecnología de agentes en la que se describe sus definiciones, lenguajes de comunicación, especificación FIPA, JADE como implementación FIPA y parser XML. Además para este trabajo se ha definido e implementado una ontología de comunicación entre agentes, la misma que fue diseñada en la herramienta Protégé. En lo que se refiere al desarrollo de componentes se hizo uso de una amplía variedad de tecnologías que incluye lenguaje de programación Java, framework JADE para el desarrollo de agentes, librería JENA para manejo de ontologías, librería SAXParser para lectura de archivos XML y patrón de diseño Factory. Finalmente se describe la metodología de trabajo utilizada en el proyecto, la cual por medio de la realización de varios ciclos iterativos permitió obtener prototipos que poco a poco fueron cubriendo las necesidades del producto software.----ABSTRACT---- This work relates to the implementation of software components within the platform Computaplex, which aims to enable researchers to conduct experimental software engineering process tasks. One of the contributions to this platform technology corresponds to the development of components which are necessary for the recovery of experimental data available in different data sources, to archive this goal a mechanism able to unify the extraction of information from MySQL, Excel and SPSS files was made. Therefore, associated research groups can share and access experimental repositories that remain both locally and externally. Moreover, it has been conducted a study of agent technology in its definition is described, languages communication, FIPA, JADE and FIPA implementation and XML parser. In addition to this work, it has been defined and implemented an ontology for communication between agents, the same as was designed in the Protégé tool. In what refers to the development of components, a wide range of technologies have been made which includes Java programming language, framework JADE for agent development, JENA library for handling ontologies, SAXParser for reading XML files and Factory design pattern. Finally, describing the work methodology used in this project, which through the implementation of several iterative cycles allowed to obtain prototypes were gradually meeting the needs of the software product.

Método de desvio de obstáculos aplicado em veículo autônomo.

A operação de veículos autônomos necessita de meios para evitar colisões quando obstáculos não conhecidos previamente são interpostos em sua trajetória. Algoritmos para executar o desvio e sensores apropriados para a detecção destes obstáculos são essenciais para a operação destes veículos. Esta dissertação apresenta estudos sobre quatro algoritmos de desvio de obstáculos e tecnologia de três tipos de sensores aplicáveis à operação de veículos autônomos. Após os estudos teóricos, um dos algoritmos foi testado para a comprovação da aplicabilidade ao veículo de teste. A etapa experimental foi a realização de um programa, escrito em linguagem de programação Java, que aplicou o algoritmo Inseto 2 para o desvio de obstáculos em uma plataforma robótica (Robodeck) com o uso de sensores ultrassônicos embarcados na referida plataforma. Os experimentos foram conduzidos em ambiente fechado (indoor), bidimensional e horizontal (plano), fazendo o Robodeck executar uma trajetória. Para os testes, obstáculos foram colocados para simular situações variadas e avaliar a eficácia do algoritmo nestas configurações de caminho. O algoritmo executou o desvio dos obstáculos com sucesso e, quando havia solução para a trajetória, ela foi encontrada. Quando não havia solução, o algoritmo detectou esta situação e parou o veículo.

An efficient algorithm for partitioning parameterized polygons into rectangles

In this paper, we propose an algorithm for partitioning parameterized orthogonal polygons into rectangles. The algorithm is based on the plane-sweep technique and can be used for partitioning polygons which contain holes. The input to the algorithm consists of the contour of a parameterized polygon to be partitioned and the constraints for those parameters which reside in the contour. The algorithm uses horizontal cuts only and generates a minimum number of rectangles whose union is the original orthogonal polygon. The proposed algorithm can be used as the basis to build corner stitching data structure for parameterized VLSI layouts and has been implemented in Java programming language. Copyright © 2010 ACM, Inc.

A realtime Internet-based quality control application for hurricane surface wind observations

This thesis chronicles the design and implementation of a Internet/Intranet and database based application for the quality control of hurricane surface wind observations. A quality control session consists of selecting desired observation types to be viewed and determining a storm track based time window for viewing the data. All observations of the selected types are then plotted in a storm relative view for the chosen time window and geography is positioned for the storm-center time about which an objective analysis can be performed. Users then make decisions about data validity through visual nearest-neighbor comparison and inspection. The project employed an Object Oriented iterative development method from beginning to end and its implementation primarily features the Java programming language. ^

A realtime internet based quality control application for hurricane surface wind observations

This thesis chronicles the design and implementation of a Intemet/Intranet and database based application for the quality control of hurricane surface wind observations. A quality control session consists of selecting desired observation types to be viewed and determining a storm track based time window for viewing the data. All observations of the selected types are then plotted in a storm relative view for the chosen time window and geography is positioned for the storm-center time about which an objective analysis can be performed. Users then make decisions about data validity through visual nearestneighbor comparison and inspection. The project employed an Object Oriented iterative development method from beginning to end and its implementation primarily features the Java programming language.

Applications of a Collaborative Open Object Oriented Learning Environment to Electronics, Computing and Mathematics Education

A lightweight Java application suite has been developed and deployed allowing collaborative learning between students and tutors at remote locations. Students can engage in group activities online and also collaborate with tutors. A generic Java framework has been developed and applied to electronics, computing and mathematics education. The applications are respectively: (a) a digital circuit simulator, which allows students to collaborate in building simple or complex electronic circuits; (b) a Java programming environment where the paradigm is behavioural-based robotics, and (c) a differential equation solver useful in modelling of any complex and nonlinear dynamic system. Each student sees a common shared window on which may be added text or graphical objects and which can then be shared online. A built-in chat room supports collaborative dialogue. Students can work either in collaborative groups or else in teams as directed by the tutor. This paper summarises the technical architecture of the system as well as the pedagogical implications of the suite. A report of student evaluation is also presented distilled from use over a period of twelve months. We intend this suite to facilitate learning between groups at one or many institutions and to facilitate international collaboration. We also intend to use the suite as a tool to research the establishment and behaviour of collaborative learning groups. We shall make our software freely available to interested researchers.

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.

Characterizing neural tissues with mass spectrometry imaging via enhanced computational approaches

Neuropeptides affect the activity of the myriad of neuronal circuits in the brain. They are under tight spatial and chemical control and the dynamics of their release and catabolism directly modify neuronal network activity. Understanding neuropeptide functioning requires approaches to determine their chemical and spatial heterogeneity within neural tissue, but most imaging techniques do not provide the complete information desired. To provide chemical information, most imaging techniques used to study the nervous system require preselection and labeling of the peptides of interest; however, mass spectrometry imaging (MSI) detects analytes across a broad mass range without the need to target a specific analyte. When used with matrix-assisted laser desorption/ionization (MALDI), MSI detects analytes in the mass range of neuropeptides. MALDI MSI simultaneously provides spatial and chemical information resulting in images that plot the spatial distributions of neuropeptides over the surface of a thin slice of neural tissue. Here a variety of approaches for neuropeptide characterization are developed. Specifically, several computational approaches are combined with MALDI MSI to create improved approaches that provide spatial distributions and neuropeptide characterizations. After successfully validating these MALDI MSI protocols, the methods are applied to characterize both known and unidentified neuropeptides from neural tissues. The methods are further adapted from tissue analysis to be able to perform tandem MS (MS/MS) imaging on neuronal cultures to enable the study of network formation. In addition, MALDI MSI has been carried out over the timecourse of nervous system regeneration in planarian flatworms resulting in the discovery of two novel neuropeptides that may be involved in planarian regeneration. In addition, several bioinformatic tools are developed to predict final neuropeptide structures and associated masses that can be compared to experimental MSI data in order to make assignments of neuropeptide identities. The integration of computational approaches into the experimental design of MALDI MSI has allowed improved instrument automation and enhanced data acquisition and analysis. These tools also make the methods versatile and adaptable to new sample types.

A Java expression evaluator for nonlinear programming

Finding the optimal value for a problem is usual in many areas of knowledge where in many cases it is needed to solve Nonlinear Optimization Problems. For some of those problems it is not possible to determine the expression for its objective function and/or its constraints, they are the result of experimental procedures, might be non-smooth, among other reasons. To solve such problems it was implemented an API contained methods to solve both constrained and unconstrained problems. This API was developed to be used either locally on the computer where the application is being executed or remotely on a server. To obtain the maximum flexibility both from the programmers’ and users’ points of view, problems can be defined as a Java class (because this API was developed in Java) or as a simple text input that is sent to the API. For this last one to be possible it was also implemented on the API an expression evaluator. One of the drawbacks of this expression evaluator is that it is slower than the Java native code. In this paper it is presented a solution that combines both options: the problem can be expressed at run-time as a string of chars that are converted to Java code, compiled and loaded dynamically. To wide the target audience of the API, this new expression evaluator is also compatible with the AMPL format.

Programming Principles: Introduction to Java

In this lecture we look at key concepts in Java: how to write, compile and run Java programs, define a simple class, create a main method, and use if/else structures to define behaviour.

Programming Principles: The Java Library

In this session we point you at the Java Library, and go into some more details on how Strings work. We also introduce the HashMap class (a very useful type of collection).

Event Driven Programming in Java

Event driven programming is a way of writing a program that works by responding to things happening (rather than executing a preplanned series of tasks). It is most often used to manage more advanced user interactions, such as GUI programs. In this session we look at how event driven programming works in Java GUIs, as both an introduction to events (using MouseListeners), and also to the way that GUI programs are constructed.

WINDOWS 10 IoT SU RASPBERRY PI 2: MULTI-PARADIGM PROGRAMMING TRA JAVA E C#

Questa tesi ha come obiettivo la sperimentazione del nuovo sistema operativo Windows 10 IoT Core su tecnologia Raspberry Pi 2, verificandone la compatibilita con alcuni sensori in commercio. Tale studio viene poi applicato in un contesto di Home Intelligence al fine di creare un agente per la gestione di luci LED, in prospettiva della sua integrazione nel sistema prototipale Home Manager.