13 papers · ranked by Valyu relevance
Patrizio Dazzi
Embarrassingly parallel problems are characterised by a very small amount of information to be exchanged among the parts they are split in, during their parallel execution. As a consequence they do not require sophisticated, low-latency, high-bandwidth interconnection networks but can be efficiently computed in…
Marco D. Visser, Sean M. McMahon, Cory Merow, Philip M. Dixon + 3 more
Parallel computing divides calculations into smaller problems and solves these simultaneously, using multiple computing elements (hereafter “workers”). In the biological sciences, many computationally intensive problems are “embarrassingly parallel” , where almost all calculations can be completed in parallel. Common…
José Colmenares, Antonella Galizia, Jesús Ortiz, Andrea Clematis + 1 more
'Walter Rocchia'] The Poisson-Boltzmann equation models the electrostatic potential generated by fixed charges on a polarizable solute immersed in an ionic solution. This approach is often used in computational structural biology to estimate the electrostatic energetic component of the assembly of molecular biological…
James S. Sims, John G. Hagedorn, Peter M. Ketcham, Steven G. Satterfield + 14 more
'Steven G. Satterfield' 'Terence J. Griffin' 'William L. George' 'Howland A. Fowler' 'Barbara A. am Ende' 'Howard K. Hung' 'Robert B. Bohn' 'John E. Koontz' 'Nicos S. Martys' 'Charles E. Bouldin' 'James A. Warren' 'David L. Feder' 'Charles W. Clark' 'B. James Filla' 'Judith E. Devaney'] The rate of scientific discovery…
Gonzalo Vera, Ritsert C Jansen, Remo L Suppi
Background R is the preferred tool for statistical analysis of many bioinformaticians due in part to the increasing number of freely available analytical methods. Such methods can be quickly reused and adapted to each particular experiment. However, in experiments where large amounts of data are generated, for example…
Xiandong Meng, Yanqing Ji
This paper focuses on the latest research and critical reviews on modern computing architectures, software and hardware accelerated algorithms for bioinformatics data analysis with an emphasis on one of the most important sequence analysis applications-hidden Markov models (HMM). We show the detailed performance…
Ahmed Hadi Ali AL-Jumaili, Ravie Chandren Muniyandi, Mohammad Kamrul Hasan, Johnny Koh Siaw Paw + 2 more
Traditional parallel computing for power management systems has prime challenges such as execution time, computational complexity, and efficiency like process time and delays in power system condition monitoring, particularly consumer power consumption, weather data, and power generation for detecting and predicting…
Francois Besnier, Kevin A. Glover, Maria Anisimova
This software package provides an R-based framework to make use of multi-core computers when running analyses in the population genetics program STRUCTURE. It is especially addressed to those users of STRUCTURE dealing with numerous and repeated data analyses, and who could take advantage of an efficient script to…
James S. Sims, William L. George, Steven G. Satterfield, Howard K. Hung + 21 more
'Howard K. Hung' 'John G. Hagedorn' 'Peter M. Ketcham' 'Terence J. Griffin' 'Stanley A. Hagstrom' 'Julien C. Franiatte' 'Garnett W. Bryant' 'W. Jaskólski' 'Nicos S. Martys' 'Charles E. Bouldin' 'Vernon Simmons' 'Oliver P. Nicolas' 'James A. Warren' 'Barbara A. am Ende' 'John E. Koontz' 'B. James Filla' 'Vital G.…
Edward Kent, Stefan Hoops, Pedro Mendes
Background Mathematical modelling has become a standard technique to improve our understanding of complex biological systems. As models become larger and more complex, simulations and analyses require increasing amounts of computational power. Clusters of computers in a high-throughput computing environment can help to…
Hassan Mushtaq, Sajid Gul Khawaja, Muhammad Usman Akram, Amanullah Yasin + 3 more
Clustering is the most common method for organizing unlabeled data into its natural groups (called clusters), based on similarity (in some sense or another) among data objects. The Partitioning Around Medoids (PAM) algorithm belongs to the partitioning-based methods of clustering widely used for objects categorization…
Zeyu Xia, Canqun Yang, Chenchen Peng, Yifei Guo + 3 more
'Tao Tang' 'Yingbo Cui'] Background The advent of Single Molecule Real-Time (SMRT) sequencing has overcome many limitations of second-generation sequencing, such as limited read lengths, PCR amplification biases. However, longer reads increase data volume exponentially and high error rates make many existing alignment…
Sirilak Ketchaya, Apisit Rattanatranurak
Quicksort is an important algorithm that uses the divide and conquer concept, and it can be run to solve any problem. The performance of the algorithm can be improved by implementing this algorithm in parallel. In this paper, the parallel sorting algorithm named the Multi-Deque Partition Dual-Deque Merge Sorting…