EXPLoRA-web: linkage analysis of quantitative trait loci using bulk segregant analysis

Identification of genomic regions associated with a phenotype of interest is a fundamental step toward solving questions in biology and improving industrial research. Bulk segregant analysis (BSA) combined with high-throughput sequencing is a technique to efficiently identify these genomic regions associated with a trait of interest. However, distinguishing true from spuriously linked genomic regions and accurately delineating the genomic positions of these truly linked regions requires the use of complex statistical models currently implemented in software tools that are generally difficult to operate for non-expert users. To facilitate the exploration and analysis of data generated by bulked segregant analysis, we present EXPLoRA-web, a web service wrapped around our previously published algorithm EXPLoRA, which exploits linkage disequilibrium to increase the power and accuracy of quantitative trait loci identification in BSA analysis. EXPLoRA-web provides a user friendly interface that enables easy data upload and parallel processing of different parameter configurations. Results are provided graphically and as BED file and/or text file and the input is expected in widely used formats, enabling straightforward BSA data analysis. The web server is available at http://bioinformatics.intec.ugent.be/explora-web/

Habilidades de alto impacto para un gerente de vanguardia

Como líder de una organización el rol de un gerente ha sido objeto de estudio a través de los tiempos, por lo que en este escrito se exploraran teorías gerenciales, para analizar las habilidades que generan mayor valor dentro de una organización en el contexto actual. De allí, se plantearán las habilidades gerenciales de mayor impacto, de acuerdo al entorno y la relación con su equipo de trabajo. Es por esto, que el gerente debe estar en continuo proceso de aprendizaje y autodesarrollo, identificando sus fortalezas y debilidades, diseñando un plan de perfeccionamiento de competencias

Métodos de ingeniería web dirigidos por modelos: una revisión de literatura

RESUMEN: Este artículo presenta algunos de los métodos de ingeniería Web dirigida por modelos que se han propuesto. En él se discuten y analizan las ventajas y desventajas de dichos métodos con relación a las tendencias actuales y las mejores prácticas en la ingeniería dirigida por modelos. La idea es presentar cada método y analizar los modelos que propone para representar aplicaciones Web, los aspectos arquitectónicos en las transformaciones y el uso de tecnologías actuales de interfaz de usuario Web en el código generado. Esto se hace con el fin de vislumbrar posibles líneas de investigación para trabajos futuros en el área de la ingeniería Web dirigida por modelos.ABSTRACT: This paper presents some of the model-driven Web engineering methods that have been proposed, and discusses and analyzes the advantages and disadvantages of such methods regarding current tendencies and best practices on model-driven engineering. The idea is to present each approach and analyze the models they propose to represent Web applications, the architectural aspects in the transformations, and the use of current Web user interface technologies in the generated code. This is done in order to depict possible research lines for future works on the model-driven Web engineering area

Revisión de la literatura en el marco de un proyecto para la validación de estrategias de aprendizaje de la Geometría en ambientes apoyados con TIC

Este artículo tiene el propósito de mostrar algunos elementos que constituyen una propuesta de acercamiento al estado del arte, como marco de referencia para un proyecto de investigación enfocado al estudio de las condiciones bajo las cuales una herramienta informática permite que los estudiantes obtengan aprendizajes significativos en Geometría

An integrated platform for genome assembly, comparative genomics and management of genomic variation databases

The use of long read DNA sequencing technologies is producing an explosion of high-quality de-novo genome assemblies. The availability of these genomes represents a major step forward for evolution, population genomics, epidemiology, among other applications. A major bottleneck for many research groups continues to be the availability of tools to build and analyze the large datasets of genomes that can be produced using these technologies. In this talk, I summarize the functionalities developed by my research group in the version four of the Next Generation Sequencing Experience Platform (NGSEP) to perform a comprehensive analysis of long and short DNA sequencing reads. First, we designed new algorithms for assembly of haploid and diploid samples from long DNA sequencing reads. A minimizers table is constructed from the reads , using K-mer hash codes calculated from rankings relative to the mode of the k-mer counts distribution. Statistics collected during this process are used as features to build layout paths. For diploid samples, we integrated a reimplementation of the ReFHap algorithm to perform molecular phasing. Benchmark experiments using PacBio HiFi and Nanopore sequencing data for different species show that our solution has competitive contiguity and efficiency, as well as superior accuracy in some cases, compared to other currently used software. We also developed a functionality to perform ortholog identification and gene-based alignment of assembled genomes. Proteomes for each genome are extracted and homology relationships are efficiently predicted building indexes of aminoacid sequences by k-mer ocurrance. Then, genes are clustered in orthogroups based on the topology of the graph induced by the predicted relationships. Gene presence/absence matrices are derived from these orthogroups. If genome assemblies are provided as input, synteny relationships are identified for each pair of genomes. We also implemented algorithms to perform alignment of short and long reads to a reference genome. Based on aligned long reads, we improved the classical variants detector to detect long structural variants. Adding up these developments, NGSEP is a comprehensive tool to perform de-novo and reference-based analysis of DNA sequencing reads in a wide variety of experimental settings to solve different research goals.Book of abstract: 4th Belgrade Bioinformatics Conference, June 19-23, 202

Towards accurate detection and genotyping of expressed variants from whole transcriptome sequencing data

BACKGROUND: Massively parallel transcriptome sequencing (RNA-Seq) is becoming the method of choice for studying functional effects of genetic variability and establishing causal relationships between genetic variants and disease. However, RNA-Seq poses new technical and computational challenges compared to genome sequencing. In particular, mapping transcriptome reads onto the genome is more challenging than mapping genomic reads due to splicing. Furthermore, detection and genotyping of single nucleotide variants (SNVs) requires statistical models that are robust to variability in read coverage due to unequal transcript expression levels. RESULTS: In this paper we present a strategy to more reliably map transcriptome reads by taking advantage of the availability of both the genome reference sequence and transcript databases such as CCDS. We also present a novel Bayesian model for SNV discovery and genotyping based on quality scores. CONCLUSIONS: Experimental results on RNA-Seq data generated from blood cell tissue of three Hapmap individuals show that our methods yield increased accuracy compared to several widely used methods. The open source code implementing our methods, released under the GNU General Public License, is available at http://dna.engr.uconn.edu/software/NGSTools/

Evaluación física y mecánica de mezclas fresado y base granular para su empleo como agregados en la conformación de bases estabilizadas de pavimentos flexibles

Trabajo de InvestigaciónEl presente trabajo tiene como fin evaluar propiedades físicas y mecánicas que pueden verse afectadas al reemplazar un porcentaje de material virgen por pavimento reciclado (RAP) en un base granular convencional. Se propuso una metodología para dicha evaluación, ejecutando ciertos ensayos de laboratorio bajo la norma INVIAS 2013, obteniendo resultados representativos que permitieron realizar los respectivos análisis, comparaciones y conclusionesINTRODUCCIÓN 1. GENERALIDADES 2. METODOLOGÍA 3. RESULTADOS Y ANÁLISIS DE RESULTADOS 4. ANÁLISIS DE ALTERNATIVAS 5. CONCLUSIONES Y RECOMENDACIONES BIBLIOGRAFÍA ANEXOSPregradoIngeniero Civi

Design of an Adiabatic Calorimeter for Cementitious Mixtures by Multi-Objective Optimization

This study aims to design an adiabatic calorimeter for cementitious mixtures using NSGA-II and the Pareto optimal solution set. In this multi-objective optimization, the controller effort and heating time are selected as objective functions. Likewise, the volume and the material to be heated were chosen as decision variables. The optimal solution was selected using Nash bargaining methods. After implementing the optimal solution, the Wilcoxon test was applied to statistically validate the developed work. The measurements performed were compared with other research and it was observed an improvement in the measurement of heat of hydration in cementitious mixtures. Also, it was noted a decrease in the error in the temperature measurement

Una mirada a la corrupción extorsiva desde el punto de vista experimental

Trabajo de InvestigaciónLa presente investigación explica la relación que existe entre el nivel de corrupción cuando existe extorsión. Cuyo objetivo es diseñar y validar un estudio experimental de laboratorio que permita entender los tratamientos realizados al paper del de línea base, se desarrolló en las instalaciones de la Universidad Católica de Colombia obteniendo como resultados que la extorsión es una variable significativa en la variación de la corrupción.Trabajo de Investigación1. INTRODUCCIÓN 2. LITERATURA RELACIONADA 3. DISEÑO EXPERIMENTAL 4. ANÁLISIS DE LOS RESULTADOS 5. CONCLUSIÓN REFERENCIAS ANEXOSPregradoEconomist