A random key based genetic algorithm for the resource constrained project scheduling problem

This paper presents a genetic algorithm for the Resource Constrained Project Scheduling Problem (RCPSP). The chromosome representation of the problem is based on random keys. The schedule is constructed using a heuristic priority rule in which the priorities of the activities are defined by the genetic algorithm. The heuristic generates parameterized active schedules. The approach was tested on a set of standard problems taken from the literature and compared with other approaches. The computational results validate the effectiveness of the proposed algorithm.

Trajectory planning of redundant manipulators using genetic algorithms

The trajectory planning of redundant robots is an important area of research and efficient optimization algorithms are needed. This paper presents a new technique that combines the closed-loop pseudoinverse method with genetic algorithms. The results are compared with a genetic algorithm that adopts the direct kinematics. In both cases the trajectory planning is formulated as an optimization problem with constraints.

Dynamical modelling of a genetic algorithm

This work addresses the signal propagation and the fractional-order dynamics during the evolution of a genetic algorithm (GA). In order to investigate the phenomena involved in the GA population evolution, the mutation is exposed to excitation perturbations during some generations and the corresponding fitness variations are evaluated. Three distinct fitness functions are used to study their influence in the GA dynamics. The input and output signals are studied revealing a fractional-order dynamic evolution, characteristic of a long-term system memory.

Optimal fuzzy PID control tuned with genetic algorithms

Fuzzy logic controllers (FLC) are intelligent systems, based on heuristic knowledge, that have been largely applied in numerous areas of everyday life. They can be used to describe a linear or nonlinear system and are suitable when a real system is not known or too difficult to find their model. FLC provide a formal methodology for representing, manipulating and implementing a human heuristic knowledge on how to control a system. These controllers can be seen as artificial decision makers that operate in a closed-loop system, in real time. The main aim of this work was to develop a single optimal fuzzy controller, easily adaptable to a wide range of systems – simple to complex, linear to nonlinear – and able to control all these systems. Due to their efficiency in searching and finding optimal solution for high complexity problems, GAs were used to perform the FLC tuning by finding the best parameters to obtain the best responses. The work was performed using the MATLAB/SIMULINK software. This is a very useful tool that provides an easy way to test and analyse the FLC, the PID and the GAs in the same environment. Therefore, it was proposed a Fuzzy PID controller (FL-PID) type namely, the Fuzzy PD+I. For that, the controller was compared with the classical PID controller tuned with, the heuristic Ziegler-Nichols tuning method, the optimal Zhuang-Atherton tuning method and the GA method itself. The IAE, ISE, ITAE and ITSE criteria, used as the GA fitness functions, were applied to compare the controllers performance used in this work. Overall, and for most systems, the FL-PID results tuned with GAs were very satisfactory. Moreover, in some cases the results were substantially better than for the other PID controllers. The best system responses were obtained with the IAE and ITAE criteria used to tune the FL-PID and PID controllers.

Optimization of multi-stage amplifiers in deep-submicron CMOS using a distributed/parallel genetic algorithm

IEEE International Symposium on Circuits and Systems, pp. 724 – 727, Seattle, EUA

Seqins: a sequencing tool for educational resources

The teaching-learning process is increasingly focused on the combination of the paradigms “learning by viewing” and “learning by doing.” In this context, educational resources, either expository or evaluative, play a pivotal role. Both types of resources are interdependent and their sequencing would create a richer educational experience to the end user. However, there is a lack of tools that support sequencing essentially due to the fact that existing specifications are complex. The Seqins is a sequencing tool of digital resources that has a fairly simple sequencing model. The tool communicates through the IMS LTI specification with a plethora of e-learning systems such as learning management systems, repositories, authoring and evaluation systems. In order to validate Seqins we integrate it in an e-learning Ensemble framework instance for the computer programming learning.

Sequencing educational resources with Seqins

Existing adaptive educational hypermedia systems have been using learning resources sequencing approaches in order to enrich the learning experience. In this context, educational resources, either expository or evaluative, play a central role. However, there is a lack of tools that support sequencing essentially due to the fact that existing specifications are complex. This paper presents Seqins as a sequencing tool of digital educational resources. Seqins includes a simple and flexible sequencing model that will foster heterogeneous students to learn at different rhythms. The tool communicates through the IMS Learning Tools Interoperability specification with a plethora of e-learning systems such as learning management systems, repositories, authoring and automatic evaluation systems. In order to validate Seqins we integrate it in an e-learning Ensemble framework instance for the computer programming learning domain.

Modified Particle Swarm Optimization Applied to Integrated Demand Response and DG Resources Scheduling

The elastic behavior of the demand consumption jointly used with other available resources such as distributed generation (DG) can play a crucial role for the success of smart grids. The intensive use of Distributed Energy Resources (DER) and the technical and contractual constraints result in large-scale non linear optimization problems that require computational intelligence methods to be solved. This paper proposes a Particle Swarm Optimization (PSO) based methodology to support the minimization of the operation costs of a virtual power player that manages the resources in a distribution network and the network itself. Resources include the DER available in the considered time period and the energy that can be bought from external energy suppliers. Network constraints are considered. The proposed approach uses Gaussian mutation of the strategic parameters and contextual self-parameterization of the maximum and minimum particle velocities. The case study considers a real 937 bus distribution network, with 20310 consumers and 548 distributed generators. The obtained solutions are compared with a deterministic approach and with PSO without mutation and Evolutionary PSO, both using self-parameterization.

Multi-agent system for distributed manufacturing scheduling with genetic algorithms and tabu search

Computerized scheduling methods and computerized scheduling systems according to exemplary embodiments. A computerized scheduling method may be stored in a memory and executed on one or more processors. The method may include defining a main multi-machine scheduling problem as a plurality of single machine scheduling problems; independently solving the plurality of single machine scheduling problems thereby calculating a plurality of near optimal single machine scheduling problem solutions; integrating the plurality of near optimal single machine scheduling problem solutions into a main multi-machine scheduling problem solution; and outputting the main multi-machine scheduling problem solution.

Integrated Management of IaaS Resources

This paper proposes and reports the development of an open source solution for the integrated management of Infrastructure as a Service (IaaS) cloud computing resources, through the use of a common API taxonomy, to incorporate open source and proprietary platforms. This research included two surveys on open source IaaS platforms (OpenNebula, OpenStack and CloudStack) and a proprietary platform (Parallels Automation for Cloud Infrastructure - PACI) as well as on IaaS abstraction solutions (jClouds, Libcloud and Deltacloud), followed by a thorough comparison to determine the best approach. The adopted implementation reuses the Apache Deltacloud open source abstraction framework, which relies on the development of software driver modules to interface with different IaaS platforms, and involved the development of a new Deltacloud driver for PACI. The resulting interoperable solution successfully incorporates OpenNebula, OpenStack (reuses pre-existing drivers) and PACI (includes the developed Deltacloud PACI driver) nodes and provides a Web dashboard and a Representational State Transfer (REST) interface library. The results of the exchanged data payload and time response tests performed are presented and discussed. The conclusions show that open source abstraction tools like Deltacloud allow the modular and integrated management of IaaS platforms (open source and proprietary), introduce relevant time and negligible data overheads and, as a result, can be adopted by Small and Medium-sized Enterprise (SME) cloud providers to circumvent the vendor lock-in problem whenever service response time is not critical.

Estrogen receptor dependent genetic and epigenetic factors of tamoxifen resistance

Resumo: A decisão da terapêutica hormonal no tratamento do cancro da mama baseiase na determinação do receptor de estrogénio alfa por imunohistoquímica (IHC). Contudo, a presença deste receptor não prediz a resposta em todas as situações, em parte devido a limitações do método IHC. Investigámos se a expressão dos genes ESR1 e ESR2, bem como a metilação dos respectivos promotores, pode estar relacionada com a evolução desfavorável de uma proporção de doentes tratados com tamoxifeno assim como com a perda dos receptores de estrogénio alfa (ERα) e beta (ERß). Amostras de 211 doentes com cancro da mama diagnosticado entre 1988 e 2004, fixadas em formalina e preservadas em parafina, foram utilizadas para a determinação por IHC da presença dos receptores ERα e ERß. O mRNA total do gene ESR1 e os níveis específicos do transcrito derivado do promotor C (ESR1_C), bem como dos transcritos ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 foram avaliados por Real-time PCR. Os promotores A e C do gene ESR1 e os promotores 0K e 0N do gene ESR2 foram investigados por análise de metilação dos dinucleotidos CpG usando bisulfite-PCR para análise com enzimas de restrição, ou para methylation specific PCR. Atendendo aos resultados promissores relacionados com a metilação do promotor do gene ESR1, complementamos o estudo com um método quantitativo por matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) suportado pelo software Epityper para a medição da metilação nos promotores A e C. Fez-se a avaliação da estabilidade do mRNA nas linhas celulares de cancro da mama MCF-7 e MDA-MB-231 tratadas com actinomicina D. Baixos níveis do transcrito ESR1_C associaram-se a uma melhor sobrevivência global (p = 0.017). Níveis elevados do transcrito ESR1_C associaram-se a uma resposta inferior ao tamoxifeno (HR = 2.48; CI 95% 1.24-4.99), um efeito mais pronunciado em doentes com tumores de fenótipo ERα/PgR duplamente positivo (HR = 3.41; CI 95% 1.45-8.04). A isoforma ESR1_C mostrou ter uma semi-vida prolongada, bem como uma estrutura secundária da região 5’UTR muito mais relaxada em comparação com a isoforma ESR1_A. A análise por Western-blot mostrou que ao nível da 21 proteína, a selectividade de promotores é indistinguivel. Não se detectou qualquer correlação entre os níveis das isoformas do gene ESR2 ou entre a metilação dos promotores do gene ESR2, e a detecção da proteína ERß. A metilação do promotor C do gene ESR1, e não do promotor A, foi responsável pela perda do receptor ERα. Estes resultados sugerem que os níveis do transcrito ESR1_C sejam usados como um novo potencial marcador para o prognóstico e predição de resposta ao tratamento com tamoxifeno em doentes com cancro da mama. Abstract: The decision of endocrine breast cancer treatment relies on ERα IHC-based assessment. However, ER positivity does not predict response in all cases in part due to IHC methodological limitations. We investigated whether ESR1 and ESR2 gene expression and respective promoter methylation may be related to non-favorable outcome of a proportion of tamoxifen treated patients as well as to ERα and ERß loss. Formalin-fixed paraffin-embedded breast cancer samples from 211 patients diagnosed between 1988 and 2004 were submitted to IHC-based ERα and ERß protein determination. ESR1 whole mRNA and promoter C specific transcript levels, as well as ESR2_ß1, ESR2_ß2/cx, and ESR2_ß5 transcripts were assessed by real-time PCR. ESR1 promoters A and C, and ESR2 promoters 0N and 0K were investigated by CpG methylation analysis using bisulfite-PCR for restriction analysis, or methylation specific PCR. Due to the promising results related to ESR1 promoter methylation, we have used a quantification method by matrixassisted laser desorption/ionization time-of-flight mass spectrometry (MALDITOF MS) together with Epityper software to measure methylation at promoters A and C. mRNA stability was assessed in actinomycin D treated MCF-7 and MDA-MB-231 cells. ERα protein was quantified using transiently transfected breast cancer cells. Low ESR1_C transcript levels were associated with better overall survival (p = 0.017). High levels of ESR1_C transcript were associated with non-favorable response in tamoxifen treated patients (HR = 2.48; CI 95% 1.24-4.99), an effect that was more pronounced in patients with ERα/PgR double-positive tumors (HR = 3.41; CI 95% 1.45-8.04). The ESR1_C isoform had a prolonged mRNA half-life and a more relaxed 5’UTR structure compared to ESR1_A isoform. Western-blot analysis showed that at protein level, the promoter selectivity is undistinguishable. There was no correlation between levels of ESR2 isoforms or ESR2 promoter methylation and ERß protein staining. ESR1 promoter C CpG methylation and not promoter A was responsible for ERα loss. We propose ESR1_C levels as a putative novel marker for breast cancer prognosis and prediction of tamoxifen response.

Time-domain optimization of amplifiers based on distributed genetic algorithms

Thesis presented in partial fulfillment of the requirements for the degree of Doctor of Philosophy in the subject of Electrical and Computer Engineering

Genetic structure of Neisseria meningitidis serogroup C epidemic strains in South Brazil

In the present study we report the results of an analysis, based on serotyping, multilocus enzyme electrophoresis (MEE), and ribotyping of N. meningitidis serogroup C strains isolated from patients with meningococcal disease (MD) in Rio Grande do Sul (RS) and Santa Catarina (SC) States, Brazil, as the Center of Epidemiology Control of Ministry of Health detected an increasing of MD cases due to this serogroup in the last two years (1992-1993). We have demonstrated that the MD due to N.meningitidis serogroup C strains in RS and SC States occurring in the last 4 years were caused mainly by one clone of strains (ET 40), with isolates indistinguishable by serogroup, serotype, subtype and even by ribotyping. One small number of cases that were not due to an ET 40 strains, represent closely related clones that probably are new lineages generated from the ET 40 clone referred as ET 11A complex. We have also analyzed N.meningitidis serogroup C strains isolated in the greater São Paulo in 1976 as representative of the first post epidemic year in that region. The ribotyping method, as well as MEE, could provide useful information about the clonal characteristics of those isolates and also of strains isolated in south Brazil. The strains from 1976 have more similarity with the actual endemic than epidemic strains, by the ribotyping, sulfonamide sensitivity, and MEE results. In conclusion, serotyping with monoclonal antibodies (C:2b:P1.3), MEE (ET 11 and ET 11A complex), and ribotyping by using ClaI restriction enzyme (Rb2), were useful to characterize these epidemic strains of N.meningitidis related to the increased incidence of MD in different States of south Brazil. It is mostly probable that these N.meningitidis serogroup C strains have poor or no genetic corelation with 1971-1975 epidemic serogroup C strains. The genetic similarity of members of the ET 11 and ET 11A complex were confirmed by the ribotyping method by using three restriction endonucleases.

Genetic relationships of Corynebacterium diphtheriae strains isolated from a diphtheria case and carriers by restriction fragment length polymorphism of rRNA genes

In the present study we report the results of an analysis, based on ribotyping of Corynebacterium diphtheriae intermedius strains isolated from a 9 years old child with clinical diphtheria and his 5 contacts. Quantitative analysis of RFLPs of rRNA was used to determine relatedness of these 7 C.diphtheriae strains providing support data in the diphtheria epidemiology. We have also tested those strains for toxigenicity in vitro by using the Elek's gel diffusion method and in vivo by using cell culture method on cultured monkey kidney cell (VERO cells). The hybridization results revealed that the 5 C.diphtheriae strains isolated from contacts and one isolated from the clinical case (nose case strain) had identical RFLP patterns with all 4 restriction endonucleases used, ribotype B. The genetic distance from this ribotype and ribotype A (throat case strain), that we initially assumed to be responsible for the illness of the patient, was of 0.450 showing poor genetic correlation among these two ribotypes. We found no significant differences concerned to the toxin production by using the cell culture method. In conclusion, the use of RFLPs of rRNA gene was successful in detecting minor differences in closely related toxigenic C.diphtheriae intermedius strains and providing information about genetic relationships among them.

Integrated Management of Cloud Computing Resources

Lunacloud is a cloud service provider with offices in Portugal, Spain, France and UK that focus on delivering reliable, elastic and low cost cloud Infrastructure as a Service (IaaS) solutions. The company currently relies on a proprietary IaaS platform - the Parallels Automation for Cloud Infrastructure (PACI) - and wishes to expand and integrate other IaaS solutions seamlessly, namely open source solutions. This is the challenge addressed in this thesis. This proposal, which was fostered by Eurocloud Portugal Association, contributes to the promotion of interoperability and standardisation in Cloud Computing. The goal is to investigate, propose and develop an interoperable open source solution with standard interfaces for the integrated management of IaaS Cloud Computing resources based on new as well as existing abstraction libraries or frameworks. The solution should provide bothWeb and application programming interfaces. The research conducted consisted of two surveys covering existing open source IaaS platforms and PACI (features and API) and open source IaaS abstraction solutions. The first study was focussed on the characteristics of most popular open source IaaS platforms, namely OpenNebula, OpenStack, CloudStack and Eucalyptus, as well as PACI and included a thorough inventory of the provided Application Programming Interfaces (API), i.e., offered operations, followed by a comparison of these platforms in order to establish their similarities and dissimilarities. The second study on existing open source interoperability solutions included the analysis of existing abstraction libraries and frameworks and their comparison. The approach proposed and adopted, which was supported on the conclusions of the carried surveys, reuses an existing open source abstraction solution – the Apache Deltacloud framework. Deltacloud relies on the development of software driver modules to interface with different IaaS platforms, officially provides and supports drivers to sixteen IaaS platform, including OpenNebula and OpenStack, and allows the development of new provider drivers. The latter functionality was used to develop a new Deltacloud driver for PACI. Furthermore, Deltacloud provides a Web dashboard and REpresentational State Transfer (REST) API interfaces. To evaluate the adopted solution, a test bed integrating OpenNebula, Open- Stack and PACI nodes was assembled and deployed. The tests conducted involved time elapsed and data payload measurements via the Deltacloud framework as well as via the pre-existing IaaS platform API. The Deltacloud framework behaved as expected, i.e., introduced additional delays, but no substantial overheads. Both the Web and the REST interfaces were tested and showed identical measurements. The developed interoperable solution for the seamless integration and provision of IaaS resources from PACI, OpenNebula and OpenStack IaaS platforms fulfils the specified requirements, i.e., provides Lunacloud with the ability to expand the range of adopted IaaS platforms and offers a Web dashboard and REST API for the integrated management. The contributions of this work include the surveys and comparisons made, the selection of the abstraction framework and, last, but not the least, the PACI driver developed.