Optimal clone identifier for genomic shotgun libraries: OC Identifier tool

In DNA microarray experiments, the gene fragments that are spotted on the slides are usually obtained by the synthesis of specific oligonucleotides that are able to amplify genes through PCR. Shotgun library sequences are an alternative to synthesis of primers for the study of each gene in the genome. The possibility of putting thousands of gene sequences into a single slide allows the use of shotgun clones in order to proceed with microarray analysis without a completely sequenced genome. We developed an OC Identifier tool (optimal clone identifier for genomic shotgun libraries) for the identification of unique genes in shotgun libraries based on a partially sequenced genome; this allows simultaneous use of clones in projects such as transcriptome and phylogeny studies, using comparative genomic hybridization and genome assembly. The OC Identifier tool allows comparative genome analysis, biological databases, query language in relational databases, and provides bioinformatics tools to identify clones that contain unique genes as alternatives to primer synthesis. The OC Identifier allows analysis of clones during the sequencing phase, making it possible to select genes of interest for construction of a DNA microarray. ©FUNPEC-RP.

Heuristics and meta-heuristics for lot sizing and scheduling in the soft drinks industry: A comparison study

This chapter studies a two-level production planning problem where, on each level, a lot sizing and scheduling problem with parallel machines, capacity constraints and sequence-dependent setup costs and times must be solved. The problem can be found in soft drink companies where the production process involves two interdependent levels with decisions concerning raw material storage and soft drink bottling. Models and solution approaches proposed so far are surveyed and conceptually compared. Two different approaches have been selected to perform a series of computational comparisons: an evolutionary technique comprising a genetic algorithm and its memetic version, and a decomposition and relaxation approach. © 2008 Springer-Verlag Berlin Heidelberg.

Transmission network expansion planning considering multiple generation scenarios

This paper presents a mathematical model and a methodology to solve a transmission network expansion planning problem considering open access. The methodology finds the optimal transmission network expansion plan that allows the power system to operate adequately in an environment with multiples generation scenarios. The model presented is solved using a specialized genetic algorithm. The methodology is tested in a system from the literature. ©2008 IEEE.

Planeamiento de la expansión de sistemas de transmisión considerando contingencias y demanda incierta

This paper presents a methodology and a mathematical model to solve the expansion planning problem that takes into account the effect of contingencies in the planning stage, and considers the demand as a stochastic variable within a specified range. In this way, it is possible to find a solution that minimizes the investment costs guarantying reliability and minimizing future load shedding. The mathematical model of the expansion planning can be represented by a mixed integer nonlinear programming problem. To solve this problem a specialized Genetic Algorithm combined with Linear Programming was implemented.

A combinatorial approach for transmission expansion & reactive power planning

A metaheuristic technique for solving the short-term transmission network expansion and reactive power planning problems, at the same time, in regulated power systems using the AC model is presented. The problem is solved using a real genetic algorithm (RGA). For each topology proposed by RGA an indicator is employed to identify the weak buses for new reactive power sources allocation. The fitness function is calculated using the cost of each configuration as well as constraints deviation of an AC optimal power flow (OPF) in which the minimum reactive generation of new reactive sources and the active power losses are objectives. With allocation of reactive power sources at load buses, the circuit capacity increases and the cost of installation could be decreased. The method is tested in a well known test system, presenting good results when compared with other approaches. © 2011 IEEE.

Tabu search to solve the Synchronized and Integrated Two-Level Lot Sizing and Scheduling Problem

This paper proposes a tabu search approach to solve the Synchronized and Integrated Two-Level Lot Sizing and Scheduling Problem (SITLSP). It is a real-world problem, often found in soft drink companies, where the production process has two integrated levels with decisions concerning raw material storage and soft drink bottling. Lot sizing and scheduling of raw materials in tanks and products in bottling lines must be simultaneously determined. Real data provided by a soft drink company is used to make comparisons with a previous genetic algorithm. Computational results have demonstrated that tabu search outperformed genetic algorithm in all instances. Copyright 2011 ACM.

Transmission network expansion planning considering phase-shifter transformers

This paper presents a novel mathematical model for the transmission network expansion planning problem. Main idea is to consider phase-shifter (PS) transformers as a new element of the transmission system expansion together with other traditional components such as transmission lines and conventional transformers. In this way, PS are added in order to redistribute active power flows in the system and, consequently, to diminish the total investment costs due to new transmission lines. Proposed mathematical model presents the structure of a mixed-integer nonlinear programming (MINLP) problem and is based on the standard DC model. In this paper, there is also applied a specialized genetic algorithm aimed at optimizing the allocation of candidate components in the network. Results obtained from computational simulations carried out with IEEE-24 bus system show an outstanding performance of the proposed methodology and model, indicating the technical viability of using these nonconventional devices during the planning process. Copyright © 2012 Celso T. Miasaki et al.

An Integrative Genomic and Transcriptomic Analysis Reveals Potential Targets Associated with Cell Proliferation in Uterine Leiomyomas

Background: Uterine Leiomyomas (ULs) are the most common benign tumours affecting women of reproductive age. ULs represent a major problem in public health, as they are the main indication for hysterectomy. Approximately 40-50% of ULs have non-random cytogenetic abnormalities, and half of ULs may have copy number alterations (CNAs). Gene expression microarrays studies have demonstrated that cell proliferation genes act in response to growth factors and steroids. However, only a few genes mapping to CNAs regions were found to be associated with ULs. Methodology: We applied an integrative analysis using genomic and transcriptomic data to identify the pathways and molecular markers associated with ULs. Fifty-one fresh frozen specimens were evaluated by array CGH (JISTIC) and gene expression microarrays (SAM). The CONEXIC algorithm was applied to integrate the data. Principal Findings: The integrated analysis identified the top 30 significant genes (P<0.01), which comprised genes associated with cancer, whereas the protein-protein interaction analysis indicated a strong association between FANCA and BRCA1. Functional in silico analysis revealed target molecules for drugs involved in cell proliferation, including FGFR1 and IGFBP5. Transcriptional and protein analyses showed that FGFR1 (P = 0.006 and P<0.01, respectively) and IGFBP5 (P = 0.0002 and P = 0.006, respectively) were up-regulated in the tumours when compared with the adjacent normal myometrium. Conclusions: The integrative genomic and transcriptomic approach indicated that FGFR1 and IGFBP5 amplification, as well as the consequent up-regulation of the protein products, plays an important role in the aetiology of ULs and thus provides data for potential drug therapies development to target genes associated with cellular proliferation in ULs. © 2013 Cirilo et al.

Multiobjective short-term planning of electric power distribution systems using NSGA-II

This paper presents a mixed integer nonlinear programming multiobjective model for short-term planning of distribution networks that considers in an integrated manner the following planning activities: allocation of capacitor banks; voltage regulators; the cable replacement of branches and feeders. The objective functions considered in the proposed model are: to minimize operational and investment costs and minimize the voltage deviations in the the network buses, subject to a set of technical and operational constraints. A multiobjective genetic algorithm based on a Non-Dominated Sorting Genetic Algorithm (NSGA-II) is proposed to solve this model. The proposed mathematical model and solution methodology is validated testing a medium voltage distribution system with 135 buses. © 2013 Brazilian Society for Automatics - SBA.

Modelo de programação matemática para controle do crescimento da vegetação sob redes de distribuição de energia elétrica

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Alocação otimizada de bancos de capacitores em sistemas de distribuição de energia elétrica através de metaheurísticas multiobjetivo

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Metaheurística particle swarm utilizada para alocação ótima de bancos de capacitores em sistemas de distribuição radial

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

Planejamento da expansão de sistemas de transmissão considerando a retirada de linhas de transmissão

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Times assíncronos inicializadores para o planejamento da expansão da transmissão de energia elétrica baseados no modelo híbrido linear

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)

Otimização do problema de carregamento de container usando uma metaheurística eficiente

Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)