10 papers · ranked by Valyu relevance
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…
Shuvendu K. Lahiri, Chao Wang, Daniel Schemmel, Julian Büning + 3 more
'César Rodríguez' 'David Laprell' 'Klaus Wehrle'] We describe a technique for systematic testing of multi-threaded programs. We combine Quasi-Optimal Partial-Order Reduction, a state-of-the-art technique that tackles path explosion due to interleaving non-determinism, with symbolic execution to handle data…
Ben Langmead, Christopher Wilks, Valentin Antonescu, Rone Charles
General-purpose processors can now contain many dozens of processor cores and support hundreds of simultaneous threads of execution. To make best use of these threads, genomics software must contend with new and subtle computer architecture issues. We discuss some of these and propose methods for improving thread…
Eunjae Kim, Sukwon Choi, Cheong Ghil Kim, Woo-Chan Park + 1 more
We propose a multi-threaded algorithm that can improve the performance of geometric acoustic (GA)-based sound propagation algorithms in mobile devices. In general, sound propagation algorithms require high computational cost because they perform based on ray tracing algorithms. For this reason, it is difficult to…
Tao Liu, Yi Liu, Chen Qian, Depei Qian + 1 more
With the development of multi-/many-core processors, applications need to be written as parallel programs to improve execution efficiency. For data-intensive applications that use multiple threads to read/write files simultaneously, an I/O sub-system can easily become a bottleneck when too many of these types of…
Ling-Hong Hung, Wes Lloyd, Radhika Agumbe Sridhar, Saranya Devi Athmalingam Ravishankar + 3 more
For many next-generation sequencing pipelines, the most computationally intensive step is the alignment of reads to a reference sequence. As a result, alignment software such as the Burrows-Wheeler Aligner (BWA) is optimized for speed and and is often executed in parallel on the cloud. However, there are other less…
Min Shuai, Xin Chen
Weighted gene co-expression network analysis (WGCNA) is an R package that can search highly related gene modules. The most time-consuming step of the whole analysis is to calculate the Topological Overlap Matrix (TOM) from the Adjacency Matrix in a single thread. This study changes it to multithreading. This paper uses…
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…
Shumpei Morita, Jay T. Groves
T cells can recognize a few molecules of cognate antigen amongst vastly outnumbering non-cognate ligands. The T cell receptor (TCR) differentiates antigens based on antigen-TCR binding dwell time through a kinetic proofreading process. Historically, this has been modeled as the ligated receptor undergoing a series of…
Xinwei Zhao, Eberhard Korsching
DNA and RNA nucleotide sequences are ubiquitous in all biological cells, serving as both a comprehensive library of capabilities for the cells and as an impressive regulatory system to control cellular function. The multi-alignment framework (MAF) provided in this study offers a user-friendly platform for sequence…