scholarly journals Homology sequence analysis using GPU acceleration

2018 ◽  
Author(s):  
◽  
Huan Truong
Keyword(s):  
Parallel Computing ◽  
Heterogeneous Computing ◽  
Computational Models ◽  
Operational Taxonomic Unit ◽  
Classification Problem ◽  
Processing Unit ◽  
Sequence Motifs ◽  
Biological Sequence ◽  
Sequencing Data ◽  
Central Processing

A number of problems in bioinformatics, systems biology and computational biology field require abstracting physical entities to mathematical or computational models. In such studies, the computational paradigms often involve algorithms that can be solved by the Central Processing Unit (CPU). Historically, those algorithms benefit from the advancements of computing power in the serial processing capabilities of individual CPU cores. However, the growth has slowed down over recent years, as scaling out CPU has been shown to be both cost-prohibitive and insecure. To overcome this problem, parallel computing approaches that employ the Graphics Processing Unit (GPU) have gained attention as complementing or replacing traditional CPU approaches. The premise of this research is to investigate the applicability of various parallel computing platforms to several problems in the detection and analysis of homology in biological sequence. I hypothesize that by exploiting the sheer amount of computation power and sequencing data, it is possible to deduce information from raw sequences without supplying the underlying prior knowledge to come up with an answer. I have developed such tools to perform analysis at scales that are traditionally unattainable with general-purpose CPU platforms. I have developed a method to accelerate sequence alignment on the GPU, and I used the method to investigate whether the Operational Taxonomic Unit (OTU) classification problem can be improved with such sheer amount of computational power. I have developed a method to accelerate pairwise k-mer comparison on the GPU, and I used the method to further develop PolyHomology, a framework to scaffold shared sequence motifs across large numbers of genomes to illuminate the structure of the regulatory network in yeasts. The results suggest that such approach to heterogeneous computing could help to answer questions in biology and is a viable path to new discoveries in the present and the future.

scholarly journals Comparative study of the implementation of the Lagrange interpolation algorithm on GPU and CPU using CUDA to compute the density of a material at different temperatures

2021 ◽  
Vol 119 ◽  
pp. 07002
Author(s):  
Youness Rtal ◽  
Abdelkader Hadjoudja
Keyword(s):  
Parallel Computing ◽  
Graphics Processing Units ◽  
Lagrange Interpolation ◽  
Polynomial Interpolation ◽  
Programming Model ◽  
Interpolation Method ◽  
Processing Unit ◽  
Central Processing ◽  
Computational Performance ◽  
Different Temperatures

Graphics Processing Units (GPUs) are microprocessors attached to graphics cards, which are dedicated to the operation of displaying and manipulating graphics data. Currently, such graphics cards (GPUs) occupy all modern graphics cards. In a few years, these microprocessors have become potent tools for massively parallel computing. Such processors are practical instruments that serve in developing several fields like image processing, video and audio encoding and decoding, the resolution of a physical system with one or more unknowns. Their advantages: faster processing and consumption of less energy than the power of the central processing unit (CPU). In this paper, we will define and implement the Lagrange polynomial interpolation method on GPU and CPU to calculate the sodium density at different temperatures Ti using the NVIDIA CUDA C parallel programming model. It can increase computational performance by harnessing the power of the GPU. The objective of this study is to compare the performance of the implementation of the Lagrange interpolation method on CPU and GPU processors and to deduce the efficiency of the use of GPUs for parallel computing.

scholarly journals Using Cuda and Blockchain Technologies to Recover an Encrypted Pdf File Password

2020 ◽  
pp. 54-60
Author(s):  
V. P. Kvasnikov ◽  
A. S. Dudnik ◽  
O. O. Pysarchuk ◽  
T. S. Domkiv
Keyword(s):  
Parallel Computing ◽  
Statistical Analysis ◽  
Experimental Studies ◽  
Central Processing Unit ◽  
Processing Unit ◽  
Computing Technology ◽  
Graphics Processor ◽  
Central Processing ◽  
Blockchain Technology ◽  
Computational Speed

The article presents an algorithm for using parallel computing technology using CUDA and blockchain technology to recover the password for an encrypted PDF file. The analysis and comparison of the computational speed using a graphics processor (GPU) and a central processing unit (CPU) are carried out. The testing of the implemented algorithm is carried out. A statistical analysis of the results of experimental studies is presented.

scholarly journals A Review of Parallel Heterogeneous Computing Algorithms in Power Systems

Algorithms ◽  
2021 ◽  
Vol 14 (10) ◽  
pp. 275
Author(s):  
Diego Rodriguez ◽  
Diego Gomez ◽  
David Alvarez ◽  
Sergio Rivera
Keyword(s):  
Power Systems ◽  
Power System ◽  
Graphics Processing Units ◽  
Heterogeneous Computing ◽  
System Simulation ◽  
Computational Time ◽  
Processing Unit ◽  
Power System Simulation ◽  
Central Processing ◽  
Computing Platforms

The power system expansion and the integration of technologies, such as renewable generation, distributed generation, high voltage direct current, and energy storage, have made power system simulation challenging in multiple applications. The current computing platforms employed for planning, operation, studies, visualization, and the analysis of power systems are reaching their operational limit since the complexity and size of modern power systems results in long simulation times and high computational demand. Time reductions in simulation and analysis lead to the better and further optimized performance of power systems. Heterogeneous computing—where different processing units interact—has shown that power system applications can take advantage of the unique strengths of each type of processing unit, such as central processing units, graphics processing units, and field-programmable gate arrays interacting in on-premise or cloud environments. Parallel Heterogeneous Computing appears as an alternative to reduce simulation times by optimizing multitask execution in parallel computing architectures with different processing units working together. This paper presents a review of Parallel Heterogeneous Computing techniques, how these techniques have been applied in a wide variety of power system applications, how they help reduce the computational time of modern power system simulation and analysis, and the current tendency regarding each application. We present a wide variety of approaches classified by technique and application.

Perangkat keras komputer

2020 ◽  
Author(s):  
Roudati jannah
Keyword(s):  
Data Storage ◽  
Central Processing Unit ◽  
External Memory ◽  
Storage Device ◽  
Input Device ◽  
Processing Unit ◽  
Central Processing ◽  
Output Device

Perangkat keras komputer adalah bagian dari sistem komputer sebagai perangkat yang dapat diraba, dilihat secara fisik, dan bertindak untuk menjalankan instruksi dari perangkat lunak (software). Perangkat keras komputer juga disebut dengan hardware. Hardware berperan secara menyeluruh terhadap kinerja suatu sistem komputer. Prinsipnya sistem komputer selalu memiliki perangkat keras masukan (input/input device system) – perangkat keras premprosesan (processing/central processing unit) – perangkat keras luaran (output/output device system) – perangkat tambahan yang sifatnya opsional (peripheral) dan tempat penyimpanan data (storage device system/external memory).

CENTRAL PROCESSING UNIT (CPU)

2020 ◽  
Author(s):  
Ika Milia wahyunu Siregar
Keyword(s):  
Processing System ◽  
Central Processing Unit ◽  
Processing Unit ◽  
Central Processing

Perkembangan IT di dunia sangat pesat, mulai dari perkembangan sofware hingga hardware. Teknologi sekarang telah mendominasi sebagian besar di permukaan bumi ini. Karena semakin cepatnya perkembangan Teknologi, kita sebagai pengguna bisa ketinggalan informasi mengenai teknologi baru apabila kita tidak up to date dalam pengetahuan teknologi ini. Hal itu dapat membuat kita mudah tergiur dan tertipu dengan berbagai iklan teknologi tanpa memikirkan sisi negatifnya. Sebagai pengguna dari komputer, kita sebaiknya tahu seputar mengenai komponen-komponen komputer. Komputer adalah serangkaian mesin elektronik yang terdiri dari jutaan komponen yang dapat saling bekerja sama, serta membentuk sebuah sistem kerja yang rapi dan teliti. Sistem ini kemudian digunakan untuk dapat melaksanakan pekerjaan secara otomatis, berdasarkan instruksi (program) yang diberikan kepadanya. Istilah Hardware komputer atau perangkat keras komputer, merupakan benda yang secara fisik dapat dipegang, dipindahkan dan dilihat. Central Processing System/ Central Processing Unit (CPU) adalah salah satu jenis perangkat keras yang berfungsi sebagai tempat untuk pengolahan data atau juga dapat dikatakan sebagai otak dari segala aktivitas pengolahan seperti penghitungan, pengurutan, pencarian, penulisan, pembacaan dan sebagainya.

Perangkat lunak komputer

2020 ◽  
Author(s):  
Intan khadijah simatupang
Keyword(s):  
Data Storage ◽  
Central Processing Unit ◽  
External Memory ◽  
Storage Device ◽  
Input Device ◽  
Processing Unit ◽  
Central Processing ◽  
Output Device

Komputer adalah serangkaian mesin elektronik yang terdiri dari jutaan komponen yang dapat saling bekerja sama, serta membentuk sebuah sistem kerja yang rapi dan teliti. Sistem ini kemudian digunakan untuk dapat melaksanakan pekerjaan secara otomatis, berdasarkan instruksi (program) yang diberikan kepadanya. Istilah Hardware computer atau perangkat keras komputer, merupakan benda yang secara fisik dapat dipegang, dipindahkan dan dilihat. Software komputer atau perangkat lunak komputer merupakan kumpulan instruksi (program/prosedur) untuk dapat melaksanakan pekerjaan secara otomatis dengan cara mengolah atau memproses kumpulan instruksi (data) yang diberikan. Pada prinsipnya sistem komputer selalu memiliki perangkat keras masukan (input/input device system) – perangkat keras pemprosesan (processing/ central processing unit) – perangkat keras keluaran (output/output device system), perangkat tambahan yang sifatnya opsional (peripheral) dan tempat penyimpanan data (Storage device system/external memory).

PERANGKAT KERAS ( HARDWARE ) PADA KOMPUTER

2020 ◽  
Author(s):  
Siti Kumala Dewi
Keyword(s):  
Processing System ◽  
Central Processing Unit ◽  
Input Device ◽  
Processing Unit ◽  
Central Processing ◽  
Output Device ◽  
System P ◽  
System 2

Perangkat keras komputer adalah bagian dari sistem komputer sebagai perangkat yang dapat diraba, dilihat secara fisik, dan bertindak untuk menjalankan instruksi dari perangkat lunak (software). Perangkat keras komputer juga disebut dengan hardware. Hardware berperan secara menyeluruh terhadap kinerja suatu sistem komputer. Berdasarkan fungsinya, perangkat keras terbagi menjadi :1.Sistem Perangkat Keras Masukan (Input Device System )2.Sistem Pemrosesan ( Central Processing System/ Central Processing Unit(CPU)3.Sistem Perangkat Keras Keluaran ( Output Device System )4.Sistem Perangkat Keras Tambahan (Peripheral/Accessories Device System)

Towards Computational Models of Identifying Protein Ubiquitination Sites

2019 ◽  
Vol 20 (5) ◽  
pp. 565-578 ◽  
Author(s):  
Lidong Wang ◽  
Ruijun Zhang
Keyword(s):  
Computational Methods ◽  
Computational Models ◽  
Feature Representation ◽  
Biological Sequence ◽  
Post Translational Modification ◽  
Test Dataset ◽  
Protein Ubiquitination ◽  
Protein Functions ◽  
Independent Test Dataset ◽  
Benchmark Datasets

Ubiquitination is an important post-translational modification (PTM) process for the regulation of protein functions, which is associated with cancer, cardiovascular and other diseases. Recent initiatives have focused on the detection of potential ubiquitination sites with the aid of physicochemical test approaches in conjunction with the application of computational methods. The identification of ubiquitination sites using laboratory tests is especially susceptible to the temporality and reversibility of the ubiquitination processes, and is also costly and time-consuming. It has been demonstrated that computational methods are effective in extracting potential rules or inferences from biological sequence collections. Up to the present, the computational strategy has been one of the critical research approaches that have been applied for the identification of ubiquitination sites, and currently, there are numerous state-of-the-art computational methods that have been developed from machine learning and statistical analysis to undertake such work. In the present study, the construction of benchmark datasets is summarized, together with feature representation methods, feature selection approaches and the classifiers involved in several previous publications. In an attempt to explore pertinent development trends for the identification of ubiquitination sites, an independent test dataset was constructed and the predicting results obtained from five prediction tools are reported here, together with some related discussions.

Sign in / Sign up

Export Citation Format

Share Document