A5005717412- Genomics and Phylogenetic Studies
- Algorithms and Data Compression
- Distributed and Parallel Computing Systems
- Cloud Computing and Resource Management
- Machine Learning in Bioinformatics
- Parallel Computing and Optimization Techniques
- Distributed systems and fault tolerance
- Gene expression and cancer classification
- Advanced Data Storage Technologies
- Scientific Computing and Data Management
- Peer-to-Peer Network Technologies
- IoT and Edge/Fog Computing
- Blockchain Technology Applications and Security
- Caching and Content Delivery
- RNA and protein synthesis mechanisms
- Chromosomal and Genetic Variations
- Cell Image Analysis Techniques
- Evolutionary Algorithms and Applications
- Software System Performance and Reliability
- Medical Imaging Techniques and Applications
- Genetics, Bioinformatics, and Biomedical Research
- Medical Image Segmentation Techniques
- DNA and Biological Computing
- Advanced Image and Video Retrieval Techniques
- Simulation Techniques and Applications
Universidade de Brasília
2016-2025
Universitas Nusa Bangsa
1998-2016
University of Ottawa
2009
Universidade Norte do Paraná
2008
This paper proposes and evaluates CUDAlign 4.0, a parallel strategy to obtain the optimal alignment of huge DNA sequences in multi-GPU platforms, using exact Smith–Waterman (SW) algorithm. In first phase Dynamic Programming (DP) matrix is computed by multiple GPUs, which asynchronously communicate border elements right neighbor order find score. After that, traceback SW executed. The efficient parallelization very challenging because high amount data dependency, particularly impacts...
In Genome Projects, biological sequences are aligned thousands of times, in a daily basis. The Smith-Waterman algorithm is able to retrieve the optimal local alignment with quadratic time and space complexity. So far, aligning huge sequences, such as whole chromosomes, has been regarded unfeasible, due computing memory requirements. However, high-performance platforms GPUs making it possible obtain result for reasonable time. this paper, we propose evaluate CUDAlign 2.1, parallel that uses...
O Programa Residência Pedagógica (PRP) busca integrar acadêmicos de Instituições Ensino Superior (IES) às escolas públicas, proporcionando experiências práticas para a formação docente. Este estudo, por meio uma pesquisa qualiquantitativa, analisou percepção dos residentes do subprojeto Química sobre efetividade da experimentação aliada à teoria, as dificuldades enfrentadas e formas avaliação aprendizagem. A partir aplicação um questionário com 19 participantes, os dados foram analisados...
Much remains to be understood about COVID-19, but the protective role of antibodies (Igs) is widely accepted in SARS-CoV-2 infection. Igs’ functions are mainly carried out by receptors that bind their Fc portion (FcR), and less attention has been dedicated cytoplasmic members this family. In work, we used single-cell RNA sequencing (scRNA-seq) data discern cell populations bronchoalveolar lavage fluid obtained from healthy individuals patients with mild or severe COVID-19. Then, evaluated...
Biological sequence comparison is a very important operation in Bioinformatics. Even though there do exist exact methods to compare biological sequences, these are often neglected due their quadratic time and space complexity. In order accelerate methods, many GPU algorithms were proposed the literature. Nevertheless, all of them restrict size smallest such way that Megabase genome prevented. this paper, we propose evaluate CUDAlign, algorithm able sequences with an Smith-Waterman affine gap...
Cross-species chromosome alignments can reveal ancestral relationships and may be used to identify the peculiarities of species. It is thus an important problem in Bioinformatics. So far, aligning huge sequences, such as whole chromosomes, with exact methods has been regarded unfeasible, due computing memory requirements. However, high performance platforms GPUs are being able change this scenario, making it possible obtain result for sequences reasonable time. In paper, we propose evaluate...
Abstract Motivation: Structured RNAs can be hard to search for as they often are not well conserved in their primary structure and local genomic or transcriptomic context. Thus, the need tools which particular make structural alignments of is only increasing. Results: To meet demand both large-scale screens hands on analysis through web servers, we present a new multithreaded version Foldalign. We substantially improve execution time while maintaining all previous functionalities, including...
This paper proposes and evaluates a parallel strategy to execute the exact Smith-Waterman (SW) biological sequence comparison algorithm for huge DNA sequences in multi-GPU platforms. In our strategy, computation of single SW matrix is spread over multiple GPUs, which communicate border elements neighbour, using circular buffer mechanism. We also provide method predict execution time speedup comparison, given number GPUs sizes sequences. The results obtained with large environment show that...
Summary In this paper, we conduct statistical analyses for two Amazon cloud pricing models: on demand and spot. On instances are charged a fixed price can only be terminated by the user, with very high availability. other hand, spot dynamic determined market‐driven model revoked provider when becomes higher than user‐defined price, having possibly low Our analysis on‐demand resulted in multiple linear regression equations that represent influence of characteristics processor RAM memory...
Biological sequence alignment is a very popular application in Bioinformatics, used routinely worldwide. Many implementations of biological algorithms have been proposed for multicores, GPUs, FPGAs and CellBEs. These are platform-specific; porting them to other systems requires considerable programming effort. This article proposes evaluates MASA, flexible customizable software architecture that enables the execution applications with three variants (local, global, semiglobal) multiple...
Sensitivity analysis and parameter tuning are important processes in large-scale image analysis. They very costly because the workflows required to be executed several times systematically correlate output variations with changes or tune parameters. An integrated solution minimum user interaction that uses effective methodologies high performance computing is scale these studies large imaging datasets expensive workflows.The experiments two segmentation show proposed approach can (i) quickly...
The recent and astonishing accomplishments in the field of Genomics would not have been possible without techniques, algorithms, tools developed Bioinformatics. Biological sequence comparison is an important operation Bioinformatics because it used to determine how similar two sequences are. As a result this operation, one or more alignments are produced. DIALIGN exact algorithm that uses dynamic programming obtain optimal biological quadratic space time. One effective way accelerate design...
Nowadays, cloud users face three important problems: (a) choosing one or more appropriate provider(s) to run their application(s), (b) selecting resources, which implies having enough information about the available including characteristics and constraints, (c) configuring resources. These problems are mostly due wide range of resources usually have distinct dependencies, they offered at various clouds' layers. In this complex scenario, often handle dependencies manually. This is an...
Grid computing is emerging as a new infrastructure to provide collaborative and secure resource sharing over multiple geographically distributed organizations. In this scenario, discovery very important component, since it responsible retrieve information about the resources that compose grid. Traditionally, kind of data be retrieved by mechanisms statically defined. highly heterogeneous dynamic environment such grid, defined searches are usually inappropriate. paper, we propose evaluate an...
Online social networks (OSNs) offer people the opportunity to join communities where they share a common interest or objective. This kind of community is useful for studying human behavior, diffusion information, and dynamics groups. As members are always changing, an efficient solution needed query information in real time. paper introduces Follow Model present basic relationship between users OSNs, combines it with MapReduce develop new algorithms parallel paradigms querying. Two models...
High performance platforms composed of commodity computing resources, such as grids and peer-to-peer systems, have greatly evolved assumed an important role in the last decade. Nevertheless, their wide commercial use still depends on establishment effective quality service (QoS) infrastructure those environments. For this reason, a variety proposals recently emerged which consumer provider monitor control grid resources order to guarantee previously established level agreements. However,...