Síntese e caracterização de redes metalo-orgânicas de fármacos

Trabalho Final de Mestrado para obtenção do grau de Mestre em Engenharia Química e Biológica

Pattern operators for grid

The definition and programming of distributed applications has become a major research issue due to the increasing availability of (large scale) distributed platforms and the requirements posed by the economical globalization. However, such a task requires a huge effort due to the complexity of the distributed environments: large amount of users may communicate and share information across different authority domains; moreover, the “execution environment” or “computations” are dynamic since the number of users and the computational infrastructure change in time. Grid environments, in particular, promise to be an answer to deal with such complexity, by providing high performance execution support to large amount of users, and resource sharing across different organizations. Nevertheless, programming in Grid environments is still a difficult task. There is a lack of high level programming paradigms and support tools that may guide the application developer and allow reusability of state-of-the-art solutions. Specifically, the main goal of the work presented in this thesis is to contribute to the simplification of the development cycle of applications for Grid environments by bringing structure and flexibility to three stages of that cycle through a commonmodel. The stages are: the design phase, the execution phase, and the reconfiguration phase. The common model is based on the manipulation of patterns through pattern operators, and the division of both patterns and operators into two categories, namely structural and behavioural. Moreover, both structural and behavioural patterns are first class entities at each of the aforesaid stages. At the design phase, patterns can be manipulated like other first class entities such as components. This allows a more structured way to build applications by reusing and composing state-of-the-art patterns. At the execution phase, patterns are units of execution control: it is possible, for example, to start or stop and to resume the execution of a pattern as a single entity. At the reconfiguration phase, patterns can also be manipulated as single entities with the additional advantage that it is possible to perform a structural reconfiguration while keeping some of the behavioural constraints, and vice-versa. For example, it is possible to replace a behavioural pattern, which was applied to some structural pattern, with another behavioural pattern. In this thesis, besides the proposal of the methodology for distributed application development, as sketched above, a definition of a relevant set of pattern operators was made. The methodology and the expressivity of the pattern operators were assessed through the development of several representative distributed applications. To support this validation, a prototype was designed and implemented, encompassing some relevant patterns and a significant part of the patterns operators defined. This prototype was based in the Triana environment; Triana supports the development and deployment of distributed applications in the Grid through a dataflow-based programming model. Additionally, this thesis also presents the analysis of a mapping of some operators for execution control onto the Distributed Resource Management Application API (DRMAA). This assessment confirmed the suitability of the proposed model, as well as the generality and flexibility of the defined pattern operators

Design and implementation of a behaviorally typed programming system for web services

Dissertação apresentada na Faculdade de Ciências e Tecnologia da Universidade Nova de Lisboa para a obtenção do Grau de Mestre em Engenharia Informática.

Penalty fuzzy function for derivative-free optimization

Penalty and Barrier methods are normally used to solve Nonlinear Optimization Problems constrained problems. The problems appear in areas such as engineering and are often characterised by the fact that involved functions (objective and constraints) are non-smooth and/or their derivatives are not know. This means that optimization methods based on derivatives cannot net used. A Java based API was implemented, including only derivative-free optimizationmethods, to solve both constrained and unconstrained problems, which includes Penalty and Barriers methods. In this work a new penalty function, based on Fuzzy Logic, is presented. This function imposes a progressive penalization to solutions that violate the constraints. This means that the function imposes a low penalization when the violation of the constraints is low and a heavy penalisation when the violation is high. The value of the penalization is not known in beforehand, it is the outcome of a fuzzy inference engine. Numerical results comparing the proposed function with two of the classic penalty/barrier functions are presented. Regarding the presented results one can conclude that the prosed penalty function besides being very robust also exhibits a very good performance.

Direct search optimization application programming interface with remote access

Search Optimization methods are needed to solve optimization problems where the objective function and/or constraints functions might be non differentiable, non convex or might not be possible to determine its analytical expressions either due to its complexity or its cost (monetary, computational, time,...). Many optimization problems in engineering and other fields have these characteristics, because functions values can result from experimental or simulation processes, can be modelled by functions with complex expressions or by noise functions and it is impossible or very difficult to calculate their derivatives. Direct Search Optimization methods only use function values and do not need any derivatives or approximations of them. In this work we present a Java API that including several methods and algorithms, that do not use derivatives, to solve constrained and unconstrained optimization problems. Traditional API access, by installing it on the developer and/or user computer, and remote API access to it, using Web Services, are also presented. Remote access to the API has the advantage of always allow the access to the latest version of the API. For users that simply want to have a tool to solve Nonlinear Optimization Problems and do not want to integrate these methods in applications, also two applications were developed. One is a standalone Java application and the other a Web-based application, both using the developed API.

A web-based tool to evaluate the iterative processes of direct search methods

Constrained and unconstrained Nonlinear Optimization Problems often appear in many engineering areas. In some of these cases it is not possible to use derivative based optimization methods because the objective function is not known or it is too complex or the objective function is non-smooth. In these cases derivative based methods cannot be used and Direct Search Methods might be the most suitable optimization methods. An Application Programming Interface (API) including some of these methods was implemented using Java Technology. This API can be accessed either by applications running in the same computer where it is installed or, it can be remotely accessed through a LAN or the Internet, using webservices. From the engineering point of view, the information needed from the API is the solution for the provided problem. On the other hand, from the optimization methods researchers’ point of view, not only the solution for the problem is needed. Also additional information about the iterative process is useful, such as: the number of iterations; the value of the solution at each iteration; the stopping criteria, etc. In this paper are presented the features added to the API to allow users to access to the iterative process data.

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.

Web-based application programming interface to solve nonlinear optimization problems

Nonlinear Optimization Problems are usual in many engineering fields. Due to its characteristics the objective function of some problems might not be differentiable or its derivatives have complex expressions. There are even cases where an analytical expression of the objective function might not be possible to determine either due to its complexity or its cost (monetary, computational, time, ...). In these cases Nonlinear Optimization methods must be used. An API, including several methods and algorithms to solve constrained and unconstrained optimization problems was implemented. This API can be accessed not only as traditionally, by installing it on the developer and/or user computer, but it can also be accessed remotely using Web Services. As long as there is a network connection to the server where the API is installed, applications always access to the latest API version. Also an Web-based application, using the proposed API, was developed. This application is to be used by users that do not want to integrate methods in applications, and simply want to have a tool to solve Nonlinear Optimization Problems.

Suporte à computação paralela e distribuída em Java: distribuição e execução de trabalho

Nos últimos anos começaram a ser vulgares os computadores dotados de multiprocessadores e multi-cores. De modo a aproveitar eficientemente as novas características desse hardware começaram a surgir ferramentas para facilitar o desenvolvimento de software paralelo, através de linguagens e frameworks, adaptadas a diferentes linguagens. Com a grande difusão de redes de alta velocidade, tal como Gigabit Ethernet e a última geração de redes Wi-Fi, abre-se a oportunidade de, além de paralelizar o processamento entre processadores e cores, poder em simultâneo paralelizá-lo entre máquinas diferentes. Ao modelo que permite paralelizar processamento localmente e em simultâneo distribuí-lo para máquinas que também têm capacidade de o paralelizar, chamou-se “modelo paralelo distribuído”. Nesta dissertação foram analisadas técnicas e ferramentas utilizadas para fazer programação paralela e o trabalho que está feito dentro da área de programação paralela e distribuída. Tendo estes dois factores em consideração foi proposta uma framework que tenta aplicar a simplicidade da programação paralela ao conceito paralelo distribuído. A proposta baseia-se na disponibilização de uma framework em Java com uma interface de programação simples, de fácil aprendizagem e legibilidade que, de forma transparente, é capaz de paralelizar e distribuir o processamento. Apesar de simples, existiu um esforço para a tornar configurável de forma a adaptar-se ao máximo de situações possível. Nesta dissertação serão exploradas especialmente as questões relativas à execução e distribuição de trabalho, e a forma como o código é enviado de forma automática pela rede, para outros nós cooperantes, evitando assim a instalação manual das aplicações em todos os nós da rede. Para confirmar a validade deste conceito e das ideias defendidas nesta dissertação foi implementada esta framework à qual se chamou DPF4j (Distributed Parallel Framework for JAVA) e foram feitos testes e retiradas métricas para verificar a existência de ganhos de performance em relação às soluções já existentes.

Integração Intranet – Pro/Engineer Wildfire 3.0 Via Pro/Web.Link

Mestrado em Engenharia Informática, Área de Especialização em Arquiteturas, Sistemas e Redes

CrimsonHex: a service oriented repository of specialised learning objects

The corner stone of the interoperability of eLearning systems is the standard definition of learning objects. Nevertheless, for some domains this standard is insufficient to fully describe all the assets, especially when they are used as input for other eLearning services. On the other hand, a standard definition of learning objects in not enough to ensure interoperability among eLearning systems; they must also use a standard API to exchange learning objects. This paper presents the design and implementation of a service oriented repository of learning objects called crimsonHex. This repository is fully compliant with the existing interoperability standards and supports new definitions of learning objects for specialized domains. We illustrate this feature with the definition of programming problems as learning objects and its validation by the repository. This repository is also prepared to store usage data on learning objects to tailor the presentation order and adapt it to learner profiles.

Using mobile device detection approaches to augment the accuracy of web delivery content

Recent studies of mobile Web trends show a continuous explosion of mobile-friendly content. However, the increasing number and heterogeneity of mobile devices poses several challenges for Web programmers who want to automatically get the delivery context and adapt the content to mobile devices. In this process, the devices detection phase assumes an important role where an inaccurate detection could result in a poor mobile experience for the enduser. In this paper we compare the most promising approaches for mobile device detection. Based on this study, we present an architecture for a system to detect and deliver uniform m-Learning content to students in a Higher School. We focus mainly on the devices capabilities repository manageable and accessible through an API. We detail the structure of the capabilities XML Schema that formalizes the data within the devices capabilities XML repository and the REST Web Service API for selecting the correspondent devices capabilities data according to a specific request. Finally, we validate our approach by presenting the access and usage statistics of the mobile web interface of the proposed system such as hits and new visitors, mobile platforms, average time on site and rejection rate.

Integration of e-portfolios in learning management systems

The LMS plays a decisive role in most eLearning environments. Although they integrate many useful tools for managing eLearning activities, they must also be effectively integrated with other specialized systems typically found in an educational environment such as Repositories of Learning Objects or ePortfolio Systems. Both types of systems evolved separately but in recent years the trend is to combine them, allowing the LMS to benefit from using the ePortfolio assessment features. This paper details the most common strategies for integrating an ePortfolio system into an LMS: the data, the API and the tool integration strategies. It presents a comparative study of strategies based on the technical skills, degree of coupling, security features, batch integration, development effort, status and standardization. This study is validated through the integration of two of the most representative systems on each category - respectively Mahara and Moodle.

Bridging between programming exercises formats with BabeLO

Assessment plays a vital role in learning. This is certainly the case with assessment of computer programs, both in curricular and competitive learning. The lack of a standard – or at least a widely used format – creates a modern Ba- bel tower made of Learning Objects, of assessment items that cannot be shared among automatic assessment systems. These systems whose interoperability is hindered by the lack of a common format include contest management systems, evaluation engines, repositories of learning objects and authoring tools. A prag- matical approach to remedy this problem is to create a service to convert among existing formats. A kind of translation service specialized in programming prob- lems formats. To convert programming exercises on-the-fly among the most used formats is the purpose of the BabeLO – a service to cope with the existing Babel of Learning Object formats for programming exercises. BabeLO was designed as a service to act as a middleware in a network of systems typically used in auto- matic assessment of programs. It provides support for multiple exercise formats and can be used by: evaluation engines to assess exercises regardless of its format; repositories to import exercises from various sources; authoring systems to create exercises in multiple formats or based on exercises from other sources. This paper analyses several of existing formats to highlight both their differ- ences and their similar features. Based on this analysis it presents an approach to extensible format conversion. It presents also the features of PExIL, the pivotal format in which the conversion is based; and the function definitions of the proposed service – BabeLO. Details on the design and implementation of BabeLO, including the service API and the interfaces required to extend the conversion to a new format, are also provided. To evaluate the effectiveness and efficiency of this approach this paper reports on two actual uses of BabeLO: to relocate exercises to a different repository; and to use an evaluation engine in a network of heterogeneous systems.

Personalized public transportation information

Thesis to obtain the Master of Science Degree in Computer Science and Engineering