10 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…
Sikao Guo, Nenad Korolija, Kent Milfeld, Adip Jhaveri + 3 more
Particle-based reaction-diffusion models offer a high-resolution alternative to the continuum reaction-diffusion approach, capturing the discrete and volume-excluding nature of molecules undergoing stochastic dynamics. These methods are thus uniquely capable of simulating explicit self-assembly of particles into…
Alex M. Ascension, Marcos J. Araúzo-Bravo
Big Data analysis is a discipline with a growing number of areas where huge amounts of data is extracted and analyzed. Parallelization in Python integrates Message Passing Interface via mpi4py module. Since mpi4py does not support parallelization of objects greater than 2^31^ bytes, we developed BigMPI4py, a Python…
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…
Pierre Carrier, Bill Long, Richard Walsh, Jef Dawson + 4 more
High Performance Computing (HPC) Best Practice offers opportunities to implement lessons learned in areas such as computational chemistry and physics in genomics workflows, specifically Next-Generation Sequencing (NGS) workflows. In this study we will briefly describe how distributed-memory parallelism can be an…
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…
Ashish Chapagain, Dima Abuoliem, In Ho Cho, Tongbiao Wang
Multifunctional nanosurfaces receive growing attention due to their versatile properties. Capillary force lithography (CFL) has emerged as a simple and economical method for fabricating these surfaces. In recent works, the authors proposed to leverage the evolution strategies (ES) to modify nanosurface characteristics…
J Kyle Medley, Shaik Asifullah, Joseph Hellerstein, Herbert M Sauro
Mechanistic kinetic models of biological pathways are an important tool for understanding biological systems. Constructing kinetic models requires fitting the parameters to experimental data. However, parameter fitting on these models is a non–convex, non–linear optimization problem. Many algorithms have been proposed…
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…
Christoph Stelz, Lukas Hübner, Alexandros Stamatakis
Phylogenetic trees describe the evolutionary history among biological species based on their genomic data. Maximum Likelihood (ML) based phylogenetic inference tools search for the tree and evolutionary model that best explain the observed genomic data. Given the independence of likelihood score calculations between…