scholarly journals A WORK DISTRIBUTION STRATEGY FOR GLOBAL SEQUENCE ALIGNMENT

2019 ◽  
pp. 75-81
Author(s):  
Kailash Kalare ◽  
Jitendra Tembhurne
Keyword(s):  
Sequence Alignment ◽  
Execution Time ◽  
High Speed ◽  
Global Memory ◽  
Global Alignment ◽  
Biological Sequences ◽  
Distribution Strategy ◽  
Work Distribution ◽  
Speed Up ◽  
Time Required

The sequence alignment comprises to identify similarities and dissimilarities between two given sequences. In this paper, we propose a work distribution strategy for the implementation of DNA global sequence alignment. The main objective of this work is to minimize the execution time required for DNA global alignment of large biological sequences. The proposed approach dealt the issues with the memory optimizations and minimization of execution time. We considered the biological sequences of different size to fit into the global memory of the system. The proposed strategy is implemented in shared memory architecture using OpenMP programming for large biological sequences. Parallelization using OpenMP directive is relatively easy and execute the code fast. We experimented on the Dell Precision Tower 7910 with Intel Xeon processor with 32GB RAM and 28 CPU cores. The efficient use of global memory and cache memory optimization dominate the results of execution time. The results demonstrate the significantly high speed up using OpenMP as compared with other implementations.

scholarly journals High speed BLASTN: an accelerated MegaBLAST search tool

2015 ◽  
Vol 43 (16) ◽  
pp. 7762-7768 ◽  
Author(s):  
Ying Chen ◽  
Weicai Ye ◽  
Yongdong Zhang ◽  
Yuesheng Xu
Keyword(s):  
Sequence Alignment ◽  
High Speed ◽  
Lookup Table ◽  
Local Alignment ◽  
Biological Sequences ◽  
Parallel Performance ◽  
Seeding Method ◽  
Computational Speed ◽  
Search Tool ◽  
Nucleotide Database

Abstract Sequence alignment is a long standing problem in bioinformatics. The Basic Local Alignment Search Tool (BLAST) is one of the most popular and fundamental alignment tools. The explosive growth of biological sequences calls for speedup of sequence alignment tools such as BLAST. To this end, we develop high speed BLASTN (HS-BLASTN), a parallel and fast nucleotide database search tool that accelerates MegaBLAST—the default module of NCBI-BLASTN. HS-BLASTN builds a new lookup table using the FMD-index of the database and employs an accurate and effective seeding method to find short stretches of identities (called seeds) between the query and the database. HS-BLASTN produces the same alignment results as MegaBLAST and its computational speed is much faster than MegaBLAST. Specifically, our experiments conducted on a 12-core server show that HS-BLASTN can be 22 times faster than MegaBLAST and exhibits better parallel performance than MegaBLAST. HS-BLASTN is written in C++ and the related source code is available at https://github.com/chenying2016/queries under the GPLv3 license.

Scanning x-ray fluorescence microscopy and principal component analysis

1992 ◽  
Vol 50 (2) ◽  
pp. 1752-1753
Author(s):  
Brian Cross
Keyword(s):  
Principal Component Analysis ◽  
Fluorescence Microscopy ◽  
Spatial Resolution ◽  
High Speed ◽  
Image Acquisition ◽  
Principal Component ◽  
Fluorescence Microscope ◽  
Acquisition Rate ◽  
X Ray ◽  
Speed Up

A relatively new entry, in the field of microscopy, is the Scanning X-Ray Fluorescence Microscope (SXRFM). Using this type of instrument (e.g. Kevex Omicron X-ray Microprobe), one can obtain multiple elemental x-ray images, from the analysis of materials which show heterogeneity. The SXRFM obtains images by collimating an x-ray beam (e.g. 100 μm diameter), and then scanning the sample with a high-speed x-y stage. To speed up the image acquisition, data is acquired "on-the-fly" by slew-scanning the stage along the x-axis, like a TV or SEM scan. To reduce the overhead from "fly-back," the images can be acquired by bi-directional scanning of the x-axis. This results in very little overhead with the re-positioning of the sample stage. The image acquisition rate is dominated by the x-ray acquisition rate. Therefore, the total x-ray image acquisition rate, using the SXRFM, is very comparable to an SEM. Although the x-ray spatial resolution of the SXRFM is worse than an SEM (say 100 vs. 2 μm), there are several other advantages.

Experimental Study on the Dynamic Deformation of Simply Supported Beam in Chinese High-speed Railway

2018 ◽  
Author(s):  
Gonglian Dai ◽  
Meng Wang ◽  
Tianliang Zhao ◽  
Wenshuo Liu
Keyword(s):  
High Speed ◽  
Structure Design ◽  
Dynamic Coefficient ◽  
Bridge Structure ◽  
High Speed Railway ◽  
Simply Supported Beam ◽  
Vertical Stiffness ◽  
Simply Supported ◽  
Speed Up ◽  
Design Speed

<p>At present, Chinese high-speed railway operating mileage has exceeded 20 thousand km, and the proportion of the bridge is nearly 50%. Moreover, high-speed railway design speed is constantly improving. Therefore, controlling the deformation of the bridge structure strictly is particularly important to train speed-up as well as to ensure the smoothness of the line. This paper, based on the field test, shows the vertical and transverse absolute displacements of bridge structure by field collection. What’s more, resonance speed and dynamic coefficient of bridge were studied. The results show that: the horizontal and vertical stiffness of the bridge can meet the requirements of <b>Chinese “high-speed railway design specification” (HRDS)</b>, and the structure design can be optimized. However, the dynamic coefficient may be greater than the specification suggested value. And the simply supported beam with CRTSII ballastless track has second-order vertical resonance velocity 306km/h and third-order transverse resonance velocity 312km/h by test results, which are all coincide with the theoretical resonance velocity.</p>

scholarly journals AC_ICAP: A Flexible High Speed ICAP Controller

2015 ◽  
Vol 2015 ◽  
pp. 1-15 ◽  
Author(s):  
Luis Andres Cardona ◽  
Carles Ferrer
Keyword(s):  
High Speed ◽  
Access Port ◽  
Field Programmable ◽  
Programmable Gate Arrays ◽  
Speed Up ◽  
Run Time ◽  
Ip Cores ◽  
Similar Solutions ◽  
Internal Configuration ◽  
Run Time Reconfiguration

The Internal Configuration Access Port (ICAP) is the core component of any dynamic partial reconfigurable system implemented in Xilinx SRAM-based Field Programmable Gate Arrays (FPGAs). We developed a new high speed ICAP controller, named AC_ICAP, completely implemented in hardware. In addition to similar solutions to accelerate the management of partial bitstreams and frames, AC_ICAP also supports run-time reconfiguration of LUTs without requiring precomputed partial bitstreams. This last characteristic was possible by performing reverse engineering on the bitstream. Besides, we adapted this hardware-based solution to provide IP cores accessible from the MicroBlaze processor. To this end, the controller was extended and three versions were implemented to evaluate its performance when connected to Peripheral Local Bus (PLB), Fast Simplex Link (FSL), and AXI interfaces of the processor. In consequence, the controller can exploit the flexibility that the processor offers but taking advantage of the hardware speed-up. It was implemented in both Virtex-5 and Kintex7 FPGAs. Results of reconfiguration time showed that run-time reconfiguration of single LUTs in Virtex-5 devices was performed in less than 5 μs which implies a speed-up of more than 380x compared to the Xilinx XPS_HWICAP controller.

scholarly journals The effect of a lack of uncapped brood on social interactions between honey bee workers and the queen

Apidologie ◽  
2021 ◽  
Author(s):  
Sylwia Łopuch ◽  
Adam Tofilski
Keyword(s):  
Social Interactions ◽  
Honey Bee ◽  
Honey Bees ◽  
High Speed ◽  
Egg Production ◽  
Social Contexts ◽  
The Other ◽  
High Speed Camera ◽  
Time Required ◽  
Honey Bee Workers

AbstractVibro-acoustic communication is used by honey bees in many different social contexts. Our previous research showed that workers interact with their queen outside of the swarming period by means of wing-beating behaviour. Therefore, the aim of this study was to verify the hypothesis that the wing-beating behaviour of workers attending the queen stimulates her to lay eggs. The behaviour of workers and the queen was recorded using a high-speed camera, at first in the presence of uncapped brood in the nest and then without one. None of the queens performed wing-beating behaviour. On the other hand, the workers attending the queen demonstrated this behaviour two times per minute, on average, even in the presence of uncapped brood in the nest. After removing the combs with the uncapped brood, the incidence of wing-beating behaviour increased significantly to an average of four times per minute. Wing-beating behaviour did not differ significantly in its characteristics when uncapped brood was present or absent in the nest. During 3 days after removing the combs with the uncapped brood, there was no significant increase in the rate of egg lying by the queen. Therefore, the results presented here do not convincingly confirm that the wing-beating behaviour of workers affects the rate of queen's egg-lying. This negative result can be related to colony disturbance and longer time required by the queen to increase egg production.

scholarly journals HILL CIPHER ON SHAMIR’S THREE PASS PROTOCOL

2017 ◽  
Author(s):  
hasdiana
Keyword(s):  
Matrix Element ◽  
Execution Time ◽  
Invertible Matrix ◽  
Multidisciplinary Research ◽  
The Third ◽  
Xor Operation ◽  
Hill Cipher ◽  
The Matrix ◽  
Level Of Difficulty ◽  
Time Required

This preprint has been presented in the 3rd International Conference on Multidisciplinary Research, Medan, october 16 – 18, 2014---In this study the authors use the scheme of Shamir's Three Pass Protocol for Hill Cipher operation. Scheme of Shamir's Three Pass Protocol is an attractive scheme that allows senders and receivers to communicate without the key exchange. Hill Cipher is chosen because of the key-shaped matrix, which is expected to complicate the various techniques of cryptanalyst. The results of this study indicate that the weakness of the scheme of Shamir's Three Pass Protocol for XOR operation is not fully valid if it is used for Hill Cipher operations. Cryptanalyst can utilize only the third ciphertext that invertible. Matrix transpose techniques in the ciphertext aims to difficulties in solving this algorithm. The original ciphertext generated in each process is different from the transmitted ciphertext. The level of difficulty increases due to the use of larger key matrix. The amount of time required for the execution of the program depends on the length of the plaintext and the value of the matrix element. Plaintext has the same length produce different execution time depending on the value of the key elements of the matrix used.

scholarly journals Intrinsic Run-time Row Hammer PUFs: Leveraging the Row Hammer Effect for Run-Time Cryptography and Improved Security

2018 ◽  
Author(s):  
Nikolaos Athanasios Anagnostopoulos ◽  
Tolga Arul ◽  
Yufan Fan ◽  
Christian Hatzfeld ◽  
André Schaller ◽  
...  
Keyword(s):  
Random Access ◽  
Physical Unclonable Functions ◽  
Generation Times ◽  
Speed Up ◽  
Run Time ◽  
Commercial Off The Shelf ◽  
Cost Efficient ◽  
Statistical Relationships ◽  
The Times ◽  
Time Required

Physical Unclonable Functions (PUFs) based on the retention times of the cells of a Dynamic Random Access Memory (DRAM) can be utilised for the implementation of cost-efficient and lightweight cryptographic protocols. However, as recent work has demonstrated, the times needed in order to generate their responses may prohibit their widespread usage. In order to address this issue, the Row Hammer PUF has been proposed by Schaller et al. [1], which leverages the row hammer effect in DRAM modules to reduce the retention times of their cells and, therefore, significantly speed up the generation times for the responses of PUFs based on these retention times. In this work, we extend the work of Schaller et al. by presenting a run-time accessible implementation of this PUF and further reducing the time required for the generation of its responses. Additionally, we also provide a more thorough investigation of the effects of temperature variations on the the Row Hammer PUF and briefly discuss potential statistical relationships between the cells used to implement it. As our results prove, the Row Hammer PUF could potentially provide an adequate level of security for Commercial Off-The-Shelf (COTS) devices, if its dependency on temperature is mitigated, and, may therefore, be commercially adopted in the near future.

scholarly journals Faster sequence alignment through GPU-accelerated restriction of the seed-and-extend search space

2014 ◽  
Author(s):  
Richard Wilton ◽  
Tamas Budavari ◽  
Ben Langmead ◽  
Sarah J Wheelan ◽  
Steven Salzberg ◽  
...  
Keyword(s):  
Sequence Alignment ◽  
High Throughput ◽  
Search Space ◽  
Computational Effort ◽  
Biological Sequences ◽  
Reduction Techniques ◽  
Software Implementations ◽  
List Processing ◽  
High Processing

Motivation: In computing pairwise alignments of biological sequences, software implementations employ a variety of heuristics that decrease the computational effort involved in computing potential alignments. A key element in achieving high processing throughput is to identify and prioritize potential alignments where high-scoring mappings can be expected. These tasks involve list-processing operations that can be efficiently performed on GPU hardware. Results: We implemented a read aligner called A21 that exploits GPU-based parallel sort and reduction techniques to restrict the number of locations where potential alignments may be found. When compared with other high-throughput aligners, this approach finds more high-scoring mappings without sacrificing speed or accuracy. A21 running on a single GPU is about 10 times faster than comparable CPU-based tools; it is also faster and more sensitive in comparison with other recent GPU-based aligners.

Rapid and Efficient Wet Fixation by the Use of Steam

1969 ◽  
Vol 39 (6) ◽  
pp. 497-504 ◽  
Author(s):  
Norman R. S. Hollies ◽  
Steven R. Chafitz ◽  
Karen A. Farquhar
Keyword(s):  
Fiber Surface ◽  
Strong Acid ◽  
Strength Properties ◽  
Fiber System ◽  
Resin Solution ◽  
Speed Up ◽  
Drying Properties ◽  
The Individual ◽  
Time Required ◽  
Finishing Processes

The impregnation of cotton fabrics with a solution consisting of strong acid and a combination of N-methylol resins having polymer-forming and cross-linking properties distinguishes the wet-fixation system from conventional durable-press processes, and this finish results in an improved balance of smoothness and strength properties during wear and laundering. Swelling of the fibers in a steam atmosphere, following padding in the resin solution can serve to speed up the impregnation process. In addition, with controls to minimize resin migration back to the fiber surface, steaming can substantially improve the efficiency of the use of resin for producing these smooth drying properties. The degree of penetration of resin is influenced by a number of process variables, such as predrying before steaming, steaming time, fabric tension and rapidity of neutralization. The optimum in fabric performance is achieved with both sufficient resin of both types in the fiber system and even distribution of resin within the individual fibers, Steaming acts to improve both these factors over that achieved in conventional hot wet fixation and so reduces the time required for wet fixation by a factor of 20–30. There is a corresponding increase in efficiency of resin use so that resin solids in the bath can be reduced two- to three-fold. These findings appear to have general application to a variety of cotton finishing processes involving fiber impregnation with reactive resins.

Integrasi Sistem Pelaporan Kerusakan Laboratorium dan SMS Gateway Untuk Realtime Notification Laporan Kerusakan Melalui SMS Dengan Pendekatan Service Oriented Architecture (SOA)

Respati ◽  
2017 ◽  
Vol 12 (3) ◽  
Author(s):  
Yudi Susanto
Keyword(s):  
High Speed ◽  
Service Oriented Architecture ◽  
Reporting System ◽  
Modern Society ◽  
Ease Of Use ◽  
Short Message ◽  
Existing Problems ◽  
Service Oriented ◽  
Speed Up ◽  
Read Rate

INTISARILayanan Pesan Singkat atau Short Message Services(SMS) merupakan salah satu layanan jaringan telepon seluler yang digunakan untuk mengirimkan pesan pendek. Kemudahan dalam penggunaannya menjadikan SMS sebagai salah satu pengirim pesan yang banyak digunakan. Menurut Jamie Tolentino dalam artikelnya yang berjudul “Why are people still using SMS in 2015?” yang dipublikasikan dihalaman thenextweb.com mengatakan bahwa SMS merupakan cara berkomunikasi yang paling efektif dalam menjangkau pengguna dengan prosentasi 90 % dibaca dalam waktu satu menit. SMS adalah satu untuk semua solusi yang membuat siapa saja (yang mempunyai nomor ponsel) dapat dijangkau. Teknologi untuk mengirim dan menerima SMS tidak bergantung pada internet berkecepatan tinggi, yang pada dasarnya membuat siapa pun dalam masyarakat dapat dijangkau.Sistem Pelaporan Kerusakan Laboratorium merupakan sebuah sistem yang digunakan untuk mencatat berbagai permasalahan yang terjadi meliputi lokasi laboratorium, nomor komputer dan detil permasalahannya. Sistem informasi ini berbasiskan web dengan harapan sistem ini dapat diakses dari komputer manapun dan kapanpun. Dengan menggunakan sistem tersebut maka dapat dilihat secara detail segala permasalahan yang terjadi pada laboratorium sehingga pengelola laboratorium dapat menyiapkan langkah-langkah untuk menanganinya. Namun pada praktiknya banyak permasalahan yang tidak diselesaikan karena informasi permasalahan tersebut tidak sampai kepada para teknisi. Hal ini disebabkan karena untuk mengakses informasi kerusakan teknisi harus login melalui komputer sehingga memakan waktu. Dengan cara pengiriman notifikasi permasalahan yang terjadi pada laboratorium melalui sms maka setiap ada laporan permasalahan yang masuk ke Sistem Pelaporan Kerusakan akan langsung diteruskan ke teknisi secara langsung melalui pesan sms tanpa harus melakukan akses ke sistem. Hal ini dapat mempercepat proses sampainya informasi permasalahan laboratorium kepada teknisi sehingga penanganan permasalahan dapat dilakukan dengan cepat.Untuk mengintegrasikan Sistem Pelaporan Kerusakan Laboratorium dengan notifikasi SMS dapat dilakukan dengan pendekatan Service Oriented Architecture (SOA) sehingga proses integrasi tidak perlu merubah sistem yang sudah ada.Kata Kunci : Sistem Informasi, Service Oriented Architecture, SOA, Kylix, SMS GatewayABSTRACTThe Short Message Services (SMS) service is one of the mobile phone network services used to deliver short messages. Ease of use makes SMS as one of the most widely used message senders. According to Jamie Tolentino in his article entitled "Why are people still using SMS in 2015?" Published on page thenextweb.com said that SMS is the most effective way to reach users, with a 90 percent read rate in minutes. SMS is a one- size- fits- all solution which makes anybody (with a mobile number) reachable.The technology for sending and receiving SMS is not reliant on high speed internet, essentially making anyone in modern society reachable.Laboratory Damage Reporting System is a system used to record various problems that occur include the location of the laboratory, computer number and details of the problem. This information system is web based in the hope that this system can be accessed from any computer and anytime. By using the system it can be viewed in detail all the problems that occur in the laboratory so that the laboratory manager can prepare the steps to handle it. But in practice many problems are not resolved because the problem information is not up to the technicians. This is because to access the information the technician must log on through the computer so that it takes time.By way of notification of problems that occur in the laboratory through sms then any existing problems report into the Laboratory Damage Reporting System will be directly forwarded to the technician directly through sms messages without having to access the system. This can speed up the process of getting the information of laboratory problems to the technician so that problem handling can be done quickly.To integrate Laboratory Hazard Reporting System with SMS notification can be done with Service Oriented Architecture (SOA) approach so that the integration process does not need to change the existing system.Keywords : Information Systems, Service Oriented Architecture, SOA, Kylix, SMS Gateway

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